Hi PDC and welcome to the forum. Sorry it's under these circumstances.
Here's some questions, hopefully to help narrow things down. Files being associated with other thoughts may not be an indicator of corruption, unless the file is invalid, or not really in the thought folder. It could be that something happened on the back end in the thought folders (in the _brain database folder under Files), as any changes or copied files in one of those folders will be reflected back in the Properties & Attachments window. Do you use synchronization software (syncs files between computers)? When did you notice this issue? Did you have any strange occurrences prior to the issue cropping up? By that I mean error messages, workstation issues, network issues? Upgrading the PB software? Have you recently copied/pasted thoughts? To a brain? From another brain? Do you make frequent brainzips? If so, if you go back to a prior brainzip can you tell when it started? What do you mean by your URL's being broken (sorry, I couldn't tell from the .pdf). Is the location correct in the Properties & Attachments window but it opens the incorrect site? Is the link corrupt? However, attached URL issues (if they are not in the thought folder, which generally they shouldn't be unless you add them as a file attachment) could indicate a database issue as the URLs reside in the database. Sorry I asked more questions than answered. Hopefully it helps narrow things down a bit.
Java SE 6