I mean, will it try to fix a duffed up bootsector when it installs the driver?
No, I suppose it will not.
The thing is, that if the bootsector is corrupt, how did it get that way?
If it was corrupted by a virus ( Do they still exist on an Atari? ) then sure enough, try to fix it by all means!
If it was because the HD is on its way out, then its not worth bothering with the drive at all anymore I'd say.
What model HD is it mate?
Who knows, maybe one of us has that drive?