diff --git a/CHANGELOG.md b/CHANGELOG.md
index ac0de72e4ab206b1ee1d875b085e9cc447f4ea2a..bc91829f9910827407f6c7529aeef4cf5f94e80b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -57,6 +57,7 @@ release.
 ### Fixed
 - Updated History constructor to check for invalid BLOB before copying History BLOB to output cube [#4966](https://github.com/DOI-USGS/ISIS3/issues/4966)
 - Updated photomet MinnaertEmpirical model to support photemplate-style PVL format [#3621](https://github.com/DOI-USGS/ISIS3/issues/3621)
+- Fixed downloadIsisData script copying existing files with every rclone download [#5245](https://github.com/DOI-USGS/ISIS3/issues/5245)
 - Fixed gaussstretch segmentation fault error and refactored gaussstretch files/tests to use gtest [#5240](https://github.com/DOI-USGS/ISIS3/issues/5240)
 - Fix matrix inversion errors in <i>findfeatures</i> due to bad FASTGEOM matrix transforms using a more robust implementation to detect these errors and throw exceptions. Images with these errors are captured and logged to the <b>TONOTMATCHED</b> file. Fixes [#4639](https://github.com/DOI-USGS/ISIS3/issues/4639)
 - Fixed <i>findfeatures</i> use of projected mosaics with correct check for <b>TargetName</b> in the Mapping labels. [#4772](https://github.com/DOI-USGS/ISIS3/issues/4772)
diff --git a/isis/config/rclone.conf b/isis/config/rclone.conf
index a40bfbfc8cff26b55624078ec867f171e59beb9c..df0bc9cd7c48b84928bdaa11257bfe443ad5d820 100644
--- a/isis/config/rclone.conf
+++ b/isis/config/rclone.conf
@@ -18,258 +18,364 @@ url = http://www.darts.isas.jaxa.jp/
 
 [sbn]
 type =http
-url =https://sbnarchive.psi.edu/pds3/
+url = https://sbnarchive.psi.edu/pds3/
 
-[control_usgs]
+[base]
+type = alias
+remote = asc_s3:asc-isisdata/usgs_data/base/
+
+[legacybase]
+type = alias
+remote = asc_s3:asc-isisdata/usgs_data/legacy_base/
+
+[control]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/control/
 
-[apollo15_usgs]
+[apollo15]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/apollo15/
 
-[apollo16_usgs]
+[apollo16]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/apollo16/
 
-[apollo17_usgs]
+[apollo17]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/apollo17/
 
-[lro_usgs]
+[lro]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/lro/
 
 [tgo_naifKernels]
-type = alias
-remote = esa:/data/SPICE/ExoMars2016/kernels/
+type = combine
+upstreams = kernels=esa:/data/SPICE/ExoMars2016/kernels/
 
 [tgo_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/tgo/
 
+[tgo]
+type = union 
+upstreams = tgo_usgs: tgo_naifKernels:
+
 [dawn_naifKernels]
-type = alias
-remote = naif:/pub/naif/DAWN/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/DAWN/kernels/
 
 [dawn_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/dawn/
 
 [dawn_pck]
-type =alias
-remote = sbn:dawn/fc/DWNCHSPG_2/GEOMETRY/
+type = combine
+upstreams = pck=sbn:dawn/fc/DWNCHSPG_2/GEOMETRY/
+
+[dawn_kernel_combine]
+type = combine
+upstreams = kernels=dawn_pck:
+
+[dawn]
+type = union
+upstreams = dawn_kernel_combine: dawn_naifKernels: dawn_usgs:
 
 [cassini_naifKernels]
-type = alias
-remote = naif:/pub/naif/CASSINI/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/CASSINI/kernels/
 
 [cassini_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/cassini/
 
+[cassini]
+type = union 
+upstreams = cassini_usgs: cassini_naifKernels:
+
 [hayabusa2_naifKernels]
-type = alias
-remote = jaxa:/pub/hayabusa2/spice_bundle/spice_kernels/
+type = combine
+upstreams = kernels=jaxa:/pub/hayabusa2/spice_bundle/spice_kernels/
 
 [hayabusa2_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/hayabusa2/
 
+[hayabusa2]
+type = union 
+upstreams = hayabusa2_usgs: hayabusa2_naifKernels:
+
 [galileo_naifKernels]
-type = alias 
-remote = naif:/pub/naif/GLL/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/GLL/kernels/
 
 [galileo_usgs]
 type = alias 
 remote = asc_s3:asc-isisdata/usgs_data/galileo/
 
+[galileo]
+type = union
+upstreams = galileo_usgs: galileo_naifKernels:
+
 [juno_naifKernels]
-type = alias
-remote = naif:/pub/naif/pds/data/jno-j_e_ss-spice-6-v1.0/jnosp_1000/data/
+type = combine
+upstreams = kernels=naif:/pub/naif/JUNO/kernels/
 
 [juno_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/juno/
 
-[lo_usgs]
+[juno]
+type = union 
+upstreams = juno_usgs: juno_naifKernels:
+
+[lo]
 type = alias 
 remote = asc_s3:asc-isisdata/usgs_data/lo/
 
 [odyssey_naifKernels]
-type = alias
-remote = naif:/pub/naif/M01/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/M01/kernels/
 
 [odyssey_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/odyssey/
 
+[odyssey]
+type = union 
+upstreams = odyssey_usgs: odyssey_naifKernels: 
+
 [mro_naifKernels]
-type = alias
-remote = naif:/pub/naif/MRO/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/MRO/kernels/
 
 [mro_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/mro/
 
+[mro]
+type = union
+upstreams = mro_usgs: mro_naifKernels:
+
 [mex_naifKernels]
-type = alias
-remote = naif:/pub/naif/MEX/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/MEX/kernels/
 
 [mex_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/mex/
 
-[legacybase_usgs]
-type = alias
-remote = asc_s3:asc-isisdata/usgs_data/legacy_base/
+[mex]
+type = union 
+upstreams = mex_usgs: mex_naifKernels:
 
 [hayabusa_naifKernels]
-type = alias
-remote = jaxa:/pub/spice/HAYABUSA/kernels/
+type = combine
+upstreams = kernels=jaxa:/pub/spice/HAYABUSA/kernels/
 
 [hayabusa_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/hayabusa/
 
+[hayabusa]
+type = union 
+upstreams = hayabusa_usgs: hayabusa_naifKernels:
+
 [chandrayaan1_naifKernels]
-type = alias
-remote = esa:/data/SPICE/CHANDRAYAAN-1/kernels/
+type = combine
+upstreams = kernels=esa:/data/SPICE/CHANDRAYAAN-1/kernels/
 
 [chandrayaan1_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/chandrayaan1/
 
+[chandrayaan1]
+type = union 
+upstreams = chandrayaan1_usgs: chandrayaan1_naifKernels:
+
 [clementine1_naifKernels]
-type = alias
-remote = naif:/pub/naif/pds/data/clem1-l-spice-6-v1.0/clsp_1000/data/
+type = combine
+upstreams = naif:/pub/naif/CLEMENTINE/kernels/
 
 [clementine1_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/clementine1/
 
+[clementine1]
+type = union
+upstreams = clementine1_usgs: clementine1_naifKernels:
+
 [kaguya_naifKernels]
-type = alias
-remote = jaxa:/pub/pds3/sln-l-spice-6-v1.0/slnsp_1000/data/
+type = combine
+upstreams = kernels=jaxa:/pub/spice/SELENE/kernels/
 
 [kaguya_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/kaguya/
 
+[kaguya]
+type = union 
+upstreams = kaguya_usgs: kaguya_naifKernels:
+
 [mariner10_naifKernels]
-type = alias
-remote = naif:/pub/naif/M10/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/M10/kernels/
 
 [mariner10_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/mariner10/
 
-[mer_usgs]
+[mariner10]
+type = union
+upstreams = mariner10_usgs: mariner10_naifKernels:
+
+[mer]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/mer/
 
 [messenger_naifKernels]
-type = alias
-remote = naif:/pub/naif/pds/data/mess-e_v_h-spice-6-v1.0/messsp_1000/data/
+type = combine
+upstreams = kernels=naif:/pub/naif/pds/data/mess-e_v_h-spice-6-v1.0/messsp_1000/data/kernels/
 
 [messenger_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/messenger/
 
+[messenger]
+type = union 
+upstreams = messenger_usgs: messenger_naifKernels:
+
 [mgs_naifKernels]
-type = alias
-remote = naif:/pub/naif/pds/data/mgs-m-spice-6-v1.0/mgsp_1000/data/
+type = combine
+upstreams = kernels=naif:/pub/naif/pds/data/mgs-m-spice-6-v1.0/mgsp_1000/data/kernels/
 
 [mgs_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/mgs/
 
+[mgs]
+type = union 
+upstreams = mgs_usgs: mgs_naifKernels:
+
 [near_naifKernels]
-type = alias
-remote = naif:/pub/naif/pds/data/near-a-spice-6-v1.0/nearsp_1000/data/
+type = combine
+upstreams = kernels=naif:/pub/naif/pds/data/near-a-spice-6-v1.0/nearsp_1000/data/
 
 [near_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/near/
 
+[near]
+type = union 
+upstreams = near_usgs: near_naifKernels:
+
 [newhorizons_naifKernels]
-type = alias
-remote = naif:/pub/naif/pds/data/nh-j_p_ss-spice-6-v1.0/nhsp_1000/data/
+type = combine
+upstreams = kernels=naif:/pub/naif/NEWHORIZONS/kernels/
 
 [newhorizons_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/newhorizons/
 
+[newhorizons]
+type = union 
+upstreams = newhorizons_usgs: newhorizons_naifKernels:
+
 [osirisrex_naifKernels]
-type = alias
-remote = naif:/pub/naif/pds/pds4/orex/orex_spice/spice_kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/pds/pds4/orex/orex_spice/spice_kernels/ 
 
 [osirisrex_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/osirisrex/
 
-[rolo_usgs]
+[osirisrex]
+type = union
+upstreams = osirisrex_usgs: osirisrex_naifKernels:
+
+[rolo]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/rolo/
 
 [rosetta_naifKernels]
-type = alias
-remote = naif:/pub/naif/ROSETTA/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/ROSETTA/kernels/
 
 [rosetta_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/rosetta/
 
+[rosetta]
+type = union 
+upstreams = rosetta_usgs: rosetta_naifKernels:
+
 [smart1_naifKernels]
-type = alias
-remote = esa:/data/SPICE/SMART-1/kernels/
+type = combine
+upstreams = kernels=esa:/data/SPICE/SMART-1/kernels/
 
 [smart1_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/smart1/
 
+[smart1]
+type = union 
+upstreams = smart1_usgs: smart1_naifKernels:
+
 [viking1_naifKernels]
-type = alias
-remote = naif:/pub/naif/VIKING/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/VIKING/kernels/
 
 [viking1_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/viking1/
 
+[viking1]
+type = union 
+upstreams = viking1_usgs: viking1_naifKernels: 
+
 [viking2_naifKernels]
-type = alias
-remote = naif:/pub/naif/VIKING/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/VIKING/kernels/
 
 [viking2_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/viking2/
 
+[viking2]
+type = union
+upstreams = viking2_usgs: viking2_naifKernels:
+
 [voyager1_naifKernels]
-type = alias
-remote = naif:/pub/naif/VOYAGER/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/VOYAGER/kernels/
 
 [voyager1_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/voyager1/
 
+[voyager1]
+type = union 
+upstreams = voyager1_usgs: voyager1_naifKernels:
+
 [voyager2_naifKernels]
-type = alias
-remote = naif:/pub/naif/VOYAGER/kernels/
+type = combine
+upstreams = kernels=naif:/pub/naif/VOYAGER/kernels/
 
 [voyager2_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/voyager2/
 
-[base_usgs]
-type = alias
-remote = asc_s3:asc-isisdata/usgs_data/base/
+[voyager2]
+type = union 
+upstreams = voyager2_usgs: voyager2_naifKernels:
 
 [msl_usgs]
 type = alias
 remote = asc_s3:asc-isisdata/usgs_data/msl/
 
 [msl_naifKernels]
-type = alias
-remote = naif:/pub/naif/MSL/kernels/
-
+type = combine
+upstreams = kernels=naif:/pub/naif/MSL/kernels/
 
+[msl]
+type = union 
+upstreams = msl_usgs: msl_naifKernels:
\ No newline at end of file
diff --git a/isis/scripts/downloadIsisData b/isis/scripts/downloadIsisData
index 6f23cce7e44a404c9784be2bbf58d3faea587ff0..6f3e00849f7846bf49d5b73f994e9faee76c735b 100755
--- a/isis/scripts/downloadIsisData
+++ b/isis/scripts/downloadIsisData
@@ -123,17 +123,14 @@ def create_rclone_arguments(destination, mission_name, parsedArgs, rclone_kwargs
         set of kernels that will be downloaded
     """
     log.debug(f"Creating RClone command for {mission_name}")
-    mission_dir_name, source_type = mission_name.replace(":", "").split("_")
+
+    mission_dir_name = mission_name
     
-    if (mission_dir_name == "legacybase"):
+    if (mission_name == "legacybase"):
         # We still want things to go into base
         mission_dir_name = "base"
-        
-    log.debug(f"Mission_dir_name: {mission_dir_name}, source_type: {source_type}")
 
-    destination = os.path.join(destination, str(mission_dir_name).replace(":",""))
-    if source_type == "naifKernels":
-        destination = os.path.join(destination, "kernels")
+    destination = os.path.join(destination, str(mission_dir_name))
 
     if args.filter: 
         filters = [f"- {arg}" for arg in args.filters]
@@ -153,7 +150,7 @@ def create_rclone_arguments(destination, mission_name, parsedArgs, rclone_kwargs
         filter_list.append("- *")
 
     filter_args = [f'--filter={item}' for item in filter_list]
-    extra_args = [f"{mission_name}",
+    extra_args = [f"{mission_name}:",
                   f"{destination}", 
                   "--progress",
                   f"--checkers={parsedArgs.num_transfers}",
@@ -189,34 +186,25 @@ def main(mission, dest, cfg_path, parsedArgs, kwargs):
         quit(-1)
     log.debug(f"Remote Sources: {config_sources}")
 
-    supported_missions = OrderedDict({})
-    for source in sorted(config_sources, key=lambda x: x.split("_")[-1]):
-        parsed_name = source.split("_")
-        # If it is a mission, it should be in the format <mission_nam>_<source_type>
-        if len(parsed_name) == 2 and parsed_name[1] in ["usgs:", "naifKernels:"]:
-            remotes_mission_name = parsed_name[0]
-            supported_missions[remotes_mission_name] = supported_missions.get(remotes_mission_name, []) + [source]
+    supported_missions = []
+    for source in config_sources:
+        if not any(x in source for x in ["_", "esa", "naif", "jaxa", "sbn"]):
+            if source != "":
+                supported_missions.append(source.replace(":", ""))
 
-    log.debug(f"Supported missions:\n {supported_missions.keys()}")
-    log.debug(f"Complete Dictionary:\n {json.dumps(supported_missions, indent=2)}")
+    log.debug(f"Supported missions:\n {supported_missions}")
 
-    if not mission in supported_missions.keys() and mission.upper() not in ("ALL", "LEGACYBASE"):
-        raise LookupError(f"{mission} is not in the list of supported missions: {supported_missions.keys()}")
+    if not mission in supported_missions and mission.upper() not in ("ALL", "LEGACYBASE"):
+        raise LookupError(f"{mission} is not in the list of supported missions: {supported_missions}")
 
-    if mission == "legacybase":
-        args = create_rclone_arguments(dest, "legacybase_usgs:", parsedArgs, kwargs)
-        rclone(command=parsedArgs.command, extra_args=args, config=cfg_path, redirect_stdout=False, redirect_stderr=False)
-    elif(mission.upper() == "ALL"):
-        supported_missions.pop("legacybase")
-        for mission, remotes in supported_missions.items():
-            for remote in remotes:
-                args = create_rclone_arguments(dest, remote, parsedArgs, kwargs)
-                rclone(command=parsedArgs.command, extra_args=args, config=cfg_path, redirect_stdout=False, redirect_stderr=False)
-    else:
-        for remote in supported_missions[mission]:
-            args = create_rclone_arguments(dest, remote,  parsedArgs, kwargs)
+    if(mission.upper() == "ALL"):
+        supported_missions.remove("legacybase")
+        for mission in supported_missions:
+            args = create_rclone_arguments(dest, mission, parsedArgs, kwargs)
             rclone(command=parsedArgs.command, extra_args=args, config=cfg_path, redirect_stdout=False, redirect_stderr=False)
-
+    else:
+        args = create_rclone_arguments(dest, mission,  parsedArgs, kwargs)
+        rclone(command=parsedArgs.command, extra_args=args, config=cfg_path, redirect_stdout=False, redirect_stderr=False)
 
 if __name__ == '__main__':
     usageString = "usage: downloadIsisData mission dest [-h] [-v] [-n NUM_TRANSFERS] [--config CONFIG] [rclone flags]"