Yes and it's very easy to do with the batch converter. I am surprised that the art issue is occurring with Apple Losless though...hmmm. Since the rescan corrected it I am guessing it was just a freak thing. Mine does it on new scans sometimes and every now and then I do a full rescan and things correct.
Check out DBpoweramp's site and you will find plenty of info on the tools including the converter. They have a useful forum as well.