Presumably what you would do is as follows, not in any fixed order:
- Update to the latest version of fences
- back up and restore your arrangement and look for errors and correct them. This would be normal because Fences does not automatically build or rebuild its database - it has to be built. Except on initial install in a limited way, or when you drag a folder to the desktop (see below.)
- shut down fences and make your changes
- find a program that will force unlocking of files and folders. It will work thru the context menu on an entire folder or a single file. It will also rename, delete, or move the same way.
ONE MORE THING MOST IMPORTANT
A folder portal is by definition not operating directly on the desktop. Therefore it relies upon a path to the folder in question. If the path changes in any way, no matter how slight, because these are not self-healing (windows shortcuts can self-heal, and there are utilities to assist with that,) you end up with non-existent folders and the portals show up empty.
You don't have to delete them, however, or "purge" anything - you just have to manually re-link each folder portal to its new folder. This won't change the name on the folder portal but it should update your contents, since that is how it's supposed to work.
Fences on the other hand will simply mirror what you drag into them, and not change anything. If you do this only from the desktop, which is reasonable because that is the intended purpose, -- no matter how many times you copy or create shortcuts - they will all remain on the desktop. Remember that is what the desktop is for. You organize bulk in drawers and folders and have key stuff and temporary stuff on the desktop. It works fine for that.
Note that when folders and files seem to be in a fence - they will not be VISIBLE on the desktop - but in reality they are still there. You can verify this by searching for any such file or folder using Windows Explorer. So you can never screw them up. If they disappear from a fence because you renamed that file or folder - they should just become visible on the desktop.