How to Refresh Organizer Files

David said:

However, there is some corruption in the metadata somewhere because in several cases even when I point a file to it's new location, it says it cannot connect.

If you are talking about the screenshot message you have posted, the reason it can't connect is because you have imported the file already into the catalog somewhere else.  The Organizer will not allow duplicate copies of the same file to appear in the catalog.  Do a search for the file name, or part of it, (using Ctrl+Shift+K) and you should find where the connected file is.  The disconnected file will also show in the search results and if that is the case, you can then delete the disconnected file from the catalog.

David said:

I assume that if I recreate a new catalog and reimport all the photos again they will come in without the tags I ;previously created. But is it possible to export or transfer the existing tags from the old catalog into the new catalog so at least I don't have to recreate those?

The keyword tags can be imported into a new catalog.  But before I explain that in more detail, let us know whether my explanation of your screenshot solves your problem.

As Walter says, you should not manage your folders and files outside of the Organizer's catalog!  However, all is not lost.

You really haven't given us enough detail as to what you have done so far to remedy the situation, or exactly what it is that you want to do now.  So let me give you a few comments to help you find a strategy for fixing your catalog.

The "ghost" folders contain links to the files that used to be there or ones that have been renamed.  The Organizer will consider these files to be "missing."  A missing file can be one that has been deleted, renamed or moved in Explorer.

Once you delete the missing files from the "ghost" folders in the catalog (but not from the hard drive), the folders will disappear from the Folders panel. However, before you do this, you will need to make sure that the files that have been renamed and remain in the same folder have been relinked to the file with the new name.  It seem that some of this has been taken care of automatically, because you have probably found that when you click on a missing file a dialog will come up with a browser to help the program find the file and to confirm that it is the same file that was originally in the catalog.  (It is not clear whether this is the process you have engaged in.)

Part of the problem in your case is that you have deleted files from the catalog.  Do you know or can you figure out which ones you have deleted.  If so, you can safely delete the thumbnails from the catalog.

The other part of the problem is that you have moved or renamed files and folders, but you can't find some of them in the catalog.  Or do you mean that some of the missing files have been reconnected and some have not, and you are only looking for a way to reconnect the missing/disconnected files?

You can use the Find>All Missing Files menu command to search for all missing files in your catalog. This will help you know which ones are disconnected and will allow you to reconnect them. Once you have reconnected all files that have been moved or renamed, you can select the remainder (which are presumably the ones that have been deleted from your computer) and delete them from the catalog.

The reconnect process can sometimes be laborious. So, let me say again, in future DO NOT delete, move or rename any of your catalog files via Windows File Explorer.  Use only the Organizer's file management tools.

Once you import photos into the Organizer and create the catalog, ALL file and folder organization MUST be done inside the PSE Organizer. I learned this the hard way - TWICE!