I have the HDD problem under XP SP2 + Winuae 0.9.92 myself.
WinUAE can see my Conner CFA340, but it destroys the RDB, and when I try to write it using HDToolBox (OS3.9+BoingBag1) it simply does nothing, or HDToolBox reports Error 4 in drive description. This happened earlier on my A1200, but I was able to manually write back the correct RDB (3 partitions). I don't know if it is the SP2 , or should I get the BoingBag2 (BTW, the BB2 instalation that I got from the web reports a XAD error saying that the password for the archive is incorrect ?!)