I see three solutions:
1) Come up with a way for the rep to translate from the Alt-ID to the ID and then remove the Alt-ID from the card (if it was ever there).
2) Come up with a way for the software to ingest the information on the comment card and perform the translation itself, printing out new comment cards. This can be done by either typing the contents of the card into the software or scanning the entire card.
3) Get rid of comment cards.
I hope some one finds a way to make (1) or (2) work.