diff --git a/fdroidserver/deploy.py b/fdroidserver/deploy.py
index 9ef9b631..3a775847 100644
--- a/fdroidserver/deploy.py
+++ b/fdroidserver/deploy.py
@@ -96,6 +96,16 @@ def _get_index_includes(base_dir):
     return index_includes
 
 
+def _remove_missing_files(files: List[str]) -> List[str]:
+    """Remove files that are missing from the file system."""
+
+    existing = []
+    for f in files:
+        if os.path.exists(f):
+            existing.append(f)
+    return existing
+
+
 def update_awsbucket(repo_section, is_index_only=False, verbose=False, quiet=False):
     """Upload the contents of the directory `repo_section` (including subdirectories) to the AWS S3 "bucket".
 
@@ -299,8 +309,9 @@ def update_remote_storage_with_rclone(
 
     if is_index_only:
         sources = _get_index_file_paths(repo_section)
+        sources = _remove_missing_files(sources)
     else:
-        sources = repo_section
+        sources = [repo_section]
 
     for source in sources:
         if isinstance(config['rclone_config'], str):
@@ -429,6 +440,7 @@ def update_awsbucket_libcloud(repo_section, is_index_only=False):
             for name in files
         ]
         files_to_upload = list(set(files_to_upload) & set(index_files))
+        files_to_upload = _remove_missing_files(files_to_upload)
 
     else:
         files_to_upload = [
@@ -534,6 +546,9 @@ def update_serverwebroot(serverwebroot, repo_section):
     is_index_only = serverwebroot.get('index_only', False)
     logging.info('rsyncing ' + repo_section + ' to ' + url)
     if is_index_only:
+        files_to_upload = _get_index_file_paths(repo_section)
+        files_to_upload = _remove_missing_files(files_to_upload)
+
         rsyncargs += _get_index_file_paths(repo_section)
         rsyncargs += [f'{url}/{repo_section}/']
         logging.info(rsyncargs)
@@ -733,6 +748,7 @@ def update_servergitmirrors(servergitmirrors, repo_section):
             # make sure both paths have exactly one trailing slash
             if is_index_only:
                 files_to_sync = _get_index_file_paths(str(workspace_dir / repo_section))
+                files_to_sync = _remove_missing_files(files_to_sync)
             else:
                 files_to_sync = [str(workspace_dir / repo_section).rstrip('/') + '/']
             common.local_rsync(