Yep, I just confirmed it by starting up WinUAE with the ClassicWB HDF as usual, then casually strolling over to the Hard Drive settings, clicking that HDF and "accidentally" hitting the RDB mode button. Then I resetted the Amiga.
OH, NO! NO MORE CLASSICWB, just the 3.1 boot screen! Oh, what a silly sausage I am!
Just goes to show that it's most likely easier to just copy the OS to a much larger data HDF (preferably full RDB) first, process the original HDF and then copy it all back. Oh, well.