I have heard it's possible to copy data on amiga's hard disk via Winuae and I want to check SCSI hard disks with HDTune for bad sectors and SMART data.
It is, I have done this myself a few times. You need to tell WinUAE, via a setting in the harddrive options, if I remember correctly.
Then it shuld be possible to find the harddrive on the amiga/uae side using toolbox and then mount and format the drive with the proper file system..