I've had such incidence only once. The problem was that the RDB became corrupted and the SFS was ereased from it. So, yes, boot from another partition, run HDInstTools and choose "File system" to see if it's still there.
There is one SFS repairing tool for AmigaOS, but i have never used it and it doesn't look so good:
http://aminet.net/package/disk/salv/FixDisk What you have experienced with SFSDefrag shouldn't have happened. According to the first author of SFS, the defrag process suppose to be completely safe. Unlike in the ReOrg tool for FFS.
Btw, SFSDefrag is dead slow. I think it's faster to copy the contents of the partition that you want to defrag into a spare one, delete them and copy them back.
Whenever i want to defrag a partition, i use the "Defrag" tool of MorphOS. It's fast.
Edit:
The boot partition is FFS
I missed this note the first time i read your post. Is there a good reason for this?
Edit2:
It was a bad idea to try to defrag a defective partition, anyhow... What i described above, would have solved the problem with checksum errors and disk fragmentation.
