Thanks for the help finding the docs, I was able to find them. Yes, I have shut down the CCM services to run the reposcan, and no, there is no error in the event viewer. The reposcan program works, it just, like you mention, doesn't seem to find anything in the database for any of the files in the FRS.
When I went into the database to try to track down one of the file's entries, I wasn't able to find an SI_ID column. I did find SI_GUID, SI_CUID, and SI_RUID, but they are all encrypted in some way-- their values all look like "AZ0NIQgXBZNKvR3wk0KBjH4". This is in the table cms_infoobjects6. I don't know enough about the CMS database and/or BOE to get any further with a visual search.
If you have any other ideas, I'd love to hear them.