IMO, there is not a high chance that your files on the USB drive are corrupt. Over in the developers' corner, we have loads of reports of KTs simply stopping to work, or acting in weird ways.
In many cases, it seems like the *internal* databases are to blame (these are different from the files you see on the USB drive). A factory reset clears out these as well.
I suggest you simply try the approach I mentioned (you can probably limit the backup to the documents folder, but I wouldn't discriminate between files any further). It doesn't look like you have a lot to lose anyway
Edit: no, your virus scanner won't tell you if a file is corrupt. A virus scanner has a completely different purpose... it will tell you if a file is
compromised (in the sense of "dangerous"), but not if it simply contains "garbage".