Yes, the code used by the DiskTree tree control to detect changes in the folders structure has been disabled, to circumvent other problems. I will try to fix the issues, and enable again the feature in the next version release.
Even if it's not possible to see/select the updated folders structure, without restarting PDFE, you can select a, still valid, parent folder, of the ones you changed from Windows Explorer, and tick the subfolders checkbox. This way PDFE will scan the new folders structure and update the database accordingly. You can then confirm it from the DBDiskTree scan mode.