So was 3.41 the first incremental update then? I didn't really pay attention to how fast it went since I usually start the update and then go do something else.
If that's the case, then I wouldn't be surprised if the HDD upgrade issues in 3.41 were related to that.
Yes, it was the first incremental update. In theory- no, the incremental update should not have messed up the HDD in any way, just a partial vs full replace of identical (between 3.41 full and incremental) files.