diff --git a/setup_links.py b/setup_links.py
index bb4b1119a..c403ca824 100755
--- a/setup_links.py
+++ b/setup_links.py
@@ -88,6 +88,7 @@ FILES = {
   'third_party/BUILD.gn': None,
 }
 
+ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
 CHROMIUM_CHECKOUT = os.path.join('chromium', 'src')
 LINKS_DB = 'links'
 
@@ -264,6 +265,14 @@ class WebRTCLinkSetup():
           source_dir, None, check_fn=os.path.isdir,
           check_msg='directories')
 
+    if not on_bot and self._force:
+      # When making the manual switch from legacy SVN checkouts to the new
+      # Git-based Chromium DEPS, the .gclient_entries file that contains cached
+      # URLs for all DEPS entries must be removed to avoid future sync problems.
+      entries_file = os.path.join(os.path.dirname(ROOT_DIR), '.gclient_entries')
+      if os.path.exists(entries_file):
+        actions.append(Remove(entries_file, dangerous=True))
+
     actions.sort()
 
     if self._dry_run:
diff --git a/sync_chromium.py b/sync_chromium.py
index d02346c97..db6fb98ef 100755
--- a/sync_chromium.py
+++ b/sync_chromium.py
@@ -59,6 +59,12 @@ def main():
         return 0
     os.unlink(flag_file)
 
+  # To avoid gclient sync problems when DEPS entries have been removed we must
+  # wipe the .gclient_entries file that contains cached URLs for all DEPS.
+  entries_file = os.path.join(opts.chromium_dir, '.gclient_entries')
+  if os.path.exists(entries_file):
+    os.unlink(entries_file)
+
   env = os.environ.copy()
   env['GYP_CHROMIUM_NO_ACTION'] = '1'
   gclient_cmd = 'gclient.bat' if sys.platform.startswith('win') else 'gclient'