I have had the excact same problem!
1) DH0: files vansih and then the partition: My HD was too big for the orginal amiga ide controller (A4000 ide) hence writing data to the other partitions would overwrite data in the beginning of the drive! don't use any of the disk above 4GB with standard amiga IDE interface.
2) Had some trouble with getting the CV64/3D working (black screen no drive clicks), as it turns out I needed the newest drivers for the card AND for the CS MKII.
3) After I installed OS3.9 and the CV64/3D drivers "CV-drivers". I could not dobble click any of the new icons from OS3.9 it would just crash. I changed the gfx drivers to Picasso96, and volla! it worked perfektly.
anyhow.. I hope that you can use this to something.
