Indeed! Every single file except wallet.dat
.lock, addr.dat, the db text document, the debug document, the blk0001.dat file that was in there, and the blkindex.dat file. All gone.
The client re-made all the missing files and went to town.

I'm not one hundred percent on this with HYP, but for most satoshi based clients, you can force the issue. Start your daemon or QT with -bootstrap (eg /usr/local/bin/hyperstake-qt -bootstrap)
Most of them look for it anyway. And yes, always delete everything but the configuration file, bootstrap.dat, and (optionally) the wallet. I frequently do it with no wallet, and then copy my old wallet in when it's done. That way if something does go wrong, you only lose time.