How to reproduce:

1. Create a new Jenkins job
2. Enable "Clean up unused Subversion modules"
3. Add two modules from two location

   Repository URL: http://svn/repo/moduleA
   Local module directory: sub/moduleA
   
   Repository URL: http://svn/repo/moduleB
   Local module directory: sub/moduleB

4. Save job, execute it.
5. Edit job, removed moduleB
6. Save job, execute it.

What is expected:

moduleB is removed from workspace. Console output says "[WORKSPACE-CLEANER] Deleting directory 'moduleB' since it's not a configured module in SVN."

What happens:

moduleB is not removed.