Only prune non-LFS files

db/geo/migrate/20171005045404_remove_file_uploads_from_registry.rb

 class RemoveFileUploadsFromRegistry < ActiveRecord::Migration
-  # Previous to GitLab 10.0, GitLab would save attachments/avatars to the wrong
-  # directory. Destroy these entries so they will be downloaded again.
-  def change
-    Geo::FileRegistry.destroy_all
+  # Previous to GitLab 10.1, GitLab would save attachments/avatars to the
+  # wrong directory (/var/opt/gitlab/gitlab-rails/working). Destroy these
+  # entries so they will be downloaded again.
+  def up
+    Geo::BaseRegistry.connection.execute("DELETE FROM file_registry WHERE file_type != 'lfs'")
   end
 end