Files in WA, but not in Staging - not showing as modified

System

We had a branch in a state that I have never seen before, and didn't think was possible. I don't know if anyone else has written about it because I could not come up with a search string specific enough to describe it. I have no idea how we got this state to occur, but it did.

On our Production server, we have a branch where there were several hundred files in the only workarea that exists for the branch. All of the files were showing that they matched Staging - a List Modified Files at the root of the workarea displayed no modified files. However, 300+ of those files did not exist in the Staging area. So when we selected all the folders in the root of the workarea and sent them through a workflow, none of the 300+ files were submitted to Staging because TS did not think they were different than Staging, and then when we deployed (filelist deployment) from Staging, it deployed deletions for those 300+ files because they did not exist in Staging.

As you can imagine, this caused a bit of a problem on the website.

So how can this possibly happen that files can exist in the workarea but not exist in Staging and they show up with the regular old icon that implies they match Staging?