diff --git a/bin/archiver.py b/bin/archiver.py
index 34416c17..3b45a0b6 100755
--- a/bin/archiver.py
+++ b/bin/archiver.py
@@ -94,6 +94,8 @@ class Archiver(AbstractManager):
         sub_indexes: List[Path] = []
         current_index_dirs: Set[str] = set(current_index.values())
         new_captures: Set[Path] = set()
+        # Directories that are actually in the listing.
+        current_dirs: Set[str] = set()
 
         if s3fs_parent_dir:
             s3fs_dir = '/'.join([s3fs_parent_dir, root_dir.name])
@@ -117,6 +119,8 @@ class Archiver(AbstractManager):
                     # got a capture
                     if str(dir_on_disk) not in current_index_dirs:
                         new_captures.add(dir_on_disk)
+                    else:
+                        current_dirs.add(dir_on_disk.name)
 
         else:
             with os.scandir(root_dir) as it:
@@ -134,6 +138,15 @@ class Archiver(AbstractManager):
                         # isoformat
                         if str(dir_on_disk) not in current_index_dirs:
                             new_captures.add(dir_on_disk)
+                        else:
+                            current_dirs.add(dir_on_disk.name)
+
+        # Check if all the directories in current_dirs (that we got by listing the directory)
+        # are the same as the one in the index. If they're not, we pop the UUID before sriting the index
+        if current_dirs != current_index_dirs:
+            non_existing_dirs = current_index_dirs - current_dirs
+            self.logger.info(f'Got {len(non_existing_dirs)} in {root_dir}, removing them from the index.')
+            current_index = {uuid: path for uuid, path in current_index.items() if path not in non_existing_dirs}
 
         if not current_index and not new_captures and not sub_indexes:
             # No captures at all in the directory and subdirectories, quitting