Anything that was sent into México as a temporary export and cannot be returned to the U.S., must at least be accounted for. You can document lost or damaged items with a Loss/Damage Report, which should be completed and submitted (with as much back-up as possible) to your shipping coordinator or broker.
Damaged items should be returned to the U.S. if possible, even if they are to be discarded upon return. It is easier to cancel a pedimento on a damaged item (or pieces thereof) than to have to cancel the pedimento based on a report of damage. If necessary, however, the report will usually suffice.
If you cannot return (for whatever reason) items that have been damaged, take photos of them in their damaged state to attach to the Loss/Damage Report. Any additional backup to stolen items (police or security report or a notation on a daily production report) would be extremely helpful as well. A copy of the pro-forma shipping invoice the lost/damaged item(s) came into México on should also be attached to the Loss/Damage Report with the appropriate item(s) highlighted or circled.