Description of problem:

When syncing file:// repositories, files are disappearing after the sync.

Version-Release number of selected component (if applicable):

How reproducible: 100%

To Reproduce

Copy these two repositories to the FS:

https://github.com/Katello/katello/tree/master/test/fixtures/test_repos/file1
https://github.com/Katello/katello/tree/master/test/fixtures/test_repos/file2

Sync one, then the other
See that some files disappeared.

In my case, file2 lost every file except PULP_MANIFEST

Expected behavior
No files disappear.