LinkFixer Advanced can recognize and handle folder links. It is possible to use the Modify Links or Move/Rename processes on these links.

However, it is not possible to Inoculate or Cure folder links. The technical reason is that there is no metadata location data in a folder into which LinkFixer Advanced can insert our “locator beacon” identifying number (linkID). It is therefore technically impossible to use the Inoculate and Cure processes on any folder links.

After running Cure on your regular files in the new location, it should be fairly easy to write a few rename rules that would allow you to use Modify Links to change your folder links so that they point to the correct new location.