I've read every article I can find and several forums posts, most of which are flagged as answered, though none of them actually are and I still can't find a solution that will permanently and absolutely remove replication sets from FRS.
To begin with, in spite of all the research I've done both before and after deploying Server 2008r2 I somehow missed that FRS is deprecated in 2k8r2 to the point that it simply doesn't work any more for anything other than sysvol. DFSR is not an option since my 2k3 servers are all initial release, not r2.
My first reaction when finding the log entries that revealed the deprecation was to remove the replication sets in DFS management, then remove the DFS shares, and use a third party synchronization utility which has worked flawlessly elsewhere to keep directory contents synchronized for redundancy. This obviously should have been enough, but simply wasn't and isn't.
Again, I've tried everything I can find reference to including removing the database, removing the offending registry keys in all control sets, under both the replica sets subkey and the cumulative replica sets subkey, and setting the BurFlags entry to 04, all while FRS was stopped on all the other 2k3 servers.
None of the offending keys shows up on either of my 2k8 servers, so there's nothing to remove from there.
If all I had to worry about was logs filling up, I'd just cuss and move on, but unfortunately when FRS attempts to replicate, even though it fails, it moves the contents of the directory into a preexisting folder which keeps my other synchronization utility from working.
I'm hoping someone actually has an answer and will pass it along since this is taking way too much time to resolve and I have way too much to do to keep banging my head against this problem.
If I've missed anything or I'm not clear on anything, please ask and I"ll be glad to fill in the gaps.