When I attempted to update the PFS2 partitions to PSF3, it wiped all of the data and partitions (I have backups).
NEVER use HDInstTools on a disk which was partitioned by another program. While otherwise it is a great product, it has this one serious error which deletes all partitions created by other programs.
If you used HDToolbox before, keep using it. There is no need to switch to another program.
BTW, it did not wipe the data, it only deleted the partitions. If you recreate the partitions exactly as they were before, the data will reappear.
This should help you to recreate the partitions:
http://aminet.net/package/disk/salv/RDBrecovNew version:
http://thomas-rapp.homepage.t-online.de/downloads/rdbrecov.lha