Have you tried copying one of the backup directories and opening the resulting files locally to see if those "placeholders" are actually "hardlinks" to unchanged files. If they copy correctly when the entire backup directory is copied to another drive from its original server location, things are probably OK.
I have been unable to identify 20411 in the documentation, so a private message via this forum to the FM Tech Liason for this forum might be in order to ask for their team to respond.
I copied the folder to another machine over the network; the copies of those two files were still 12kb.
I also checked the contents of the RC_Data_FMS folder, to follow up on my thoughts about it being related to external container data; the source folder in the main database folder shows 5685 files, while the copy in the backup shows only 3732 files. So I'm definitely leaning towards external container files as the cause of the problem now.
Will have to try messaging the FM Tech liason; do you happen to know who that is? I tried selecting Server and Server Administraton from the Forums list, but couldn't find any reference info. (I have to admit, I haven't used the forums here much since the switchover a year or two back; I really don't care for how they're organized compared to standard web fora.)
If you use this forum's built-in Private Messaging system, you can enter for the to/contact name as "Technical Liaison" and it will reach the current FM staffer who has that job.