The 2.5" harddrive I use in my A1200 did reset itself at the same time as I did a reset of the Amiga, so the harddrive would never be detected at boottime. I could find it using HDToolBox though.
So on advice from a friend I cut off the Reset pin of the HD (I believe it was pin 1?) and now it works fine except it's not spinning up fast enough when I do a coldboot.