Well, heres my comments for what they are worth.
If I get a machine in and I (or the customer...) suspects a drive is faulty, I'll do a few checks- Assuming there are no obvious signs such as the drive clunking, then I'll run checkdisk and the manufacturers utility - some of these have a quick and an "advanced" check, I'll run the quick first, if it shows up a fault then ok the drive is faulty enough to be replaced, if it doesnt then I'll run a full check, if its still ok then as far as I'm concerned its fine, I see no other reason to do any further checks. Depending on my initial observations, and how important the data is, I may or may not clone the drive before doing anything else.
So in the issue we have here, my way above would now see the job as being complete, however this is a little different, we have 2 drives (initially 2!) with issues, both of which seem (after checks carried out) to be physically fine but the data has been corrupted, I'd be concerned about this but would be inclined to think that the corruption occured due to windows issues, however having no proof of this leaves a situation which no one likes to be in - problem fixed but no reason found.
What would I do? I would advise the customer that I had found no physical fault, and that all seems fine, I would however also advise that the problem may or may not reoccur, now if this were a home pc, I'd probably leave it at that, if it was a company pc, and downtime/data loss from this pc was critical (critical-ish - if it was that critical then 1 pc with 1 drvie wouldnt (shouldnt!) be used anyway) then I would give them the choice - but would put it to them this way - a new drive costs about £50 or so depending on size, plus fitting of course, would the machine going down again be worth more or less than £50 + fitting? more often than not if you put it that way, a new drive it is. I do the same with my equipment, for eg I recently had a backup tape that periodically failed backup, not often, but more than it ought to (i.e. never) so I replaced it, cost about £30 but you can guarantee if I hadnt, then there would have been a problem and of course the days work on that particular tape would have been the one that was needed.