How can i fix? I am sure it software
Does your HD have multiple partitions (SYS3.1, SYS3.9, Work:, APPS, etc)? Is 3.9 installed on the first partition (DH0: )?
Just to be safe, it might be wise to backup your 3.9 partition, especially those files that make your 68060 play nicely with PIV, keyfiles, registrations, etc. If it turn out your filesystem is corrupted, you can: reformat the partition, repartition and reformat the whole drive, replace the drive. If it is something simple, well, you still have backups.
Again, I hope I'm wrong. I'm trying to recover my system from what you are describing on your system. When I fixed one non-sense error, others replaced it. It was like the system had forgotten where to find things. Eventually, it spread to my other partitions too. I tried to backup too late to another HD. When I tried to move data from a bad partition to the new HD, it appeared to work until it froze. Upon reboot, no files had been moved.
Good Luck