First off, removing everything using the GUI doesn't help when the
database is corrupt. DFSR keeps the database regardless of its
membership status. So if for example you had a broken DFSR server and
removed it from every replication group, when you added it back you'd
still be out of luck.
To clear it completely after the server is no longer a member of *any*
dfsr replication group (i.e. remove it from all of them in the gui and
wait for AD replication to propgate the changes):
1. Stop the "DFS Replication" service.
2. On the drive(s) in question, grant yourself full permission to the
hidden system "System Volume Information" folder.
3. Navigate into the folder and delete (or move to be extra careful)
the DFSR folder.
4. Navigate to each replication group the server was a member of and
delete (or move to be extra careful) each hidden system "DfsrPrivate"
5. Start the "DFS Replication" service.
You may now treat the server as a brand new member for the replication
groups. Now all you need to deal with is DFSR's sloppy initial
replication routines (hint: those missing files are in the "DfsrPrivate