You could write a note, but I doubt that you'd receive anything other than an apology for the error.
Now that the correct number is on the reservation she should be on the upgrade list--I've seen enough seats open up due to mis-connects, no-shows, move-ups, etc.
Even if the correct DM miles number were on the reservation it does not necessarily mean that the upgrade would have come through. The SFO-PHL or CLT flights are often full of high status flyers. As a CP I only got upgraded once (25% last year) on those flights. When boarding for my last flight, the zone 1 boarding had to have been 40+ people (and that was after all of first boarded).
Hopefully now that her number is on there correctly a seat opens up.