@kvasir
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What I need to fix this is:
What you need is a new HD and copy the data from the old one, for which you don't have other current backups, and you have to do it as soon as possible, before your old HD dies completely.
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A block by block scan of the partition
A way to map these blocks out, I beleive this can be done with hdtoolbox, but I need a refresher on how to do this.
Both previous things that are compatable with SFS.
I'm not sure about the AmigaOS 3.9 HDToolBox, but the AmigaOS 3.1 one had an option to scan the HD and create the bad block list in the RDB. It's a software bad block list and the driver has to support it, the AmigaOS IDE scsi.device does, but if you are using a replacement like IDEFix it may not.
I wouldn't bother with it anyway, IDE HDs only return errors when they don't have any spare sectors for remapping bad sectors any more and you'll get other bad sectors, which can't be remapped by the HD any more, very soon.
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Failing that, I might be able to format the drive if sfsformat can "skip" blocks,
There are no special format programs for SFS which do that. Although there are some marking bad sectors as used for FFS partitions it's not usable with most of them for FFS either: As soon as the partition has to be validated the bad sectors marked as used will be marked as free again and you get errors again.