From a professional locksmith:
The LP line is an imported line sold at a lower price point than the safes that AMSEC actually builds themselves. There will be more problems with these types of safes due to the less expensive build quality, but AMSEC is pretty good about standing behind their products.
The warranty on the safe is similar to the warranty on a car. If you want them to pay, it has to be done on their terms. I'm assuming that you contacted AMSEC, and AMSEC was the one to dispatch the locksmith under a warranty claim.
Since I don't know what was wrong with your safe, I can't tell you why multiple holes were needed, or why it took a long time. Although this may have been justified, it's also possible that your locksmith was simply incompetent. Just like I can't rekey a deadbolt, some locksmiths can't work on safes.
As a general rule of thumb, a repair can be stronger than the safe door was originally if done properly. The pins he is talking about are taper pins, which are usually welded into place and ground smooth. Drilling a safe does not harm it, although not knowing what you're doing when drilling can harm it. I have seen plenty of "locksmiths" destroy safes because they had no clue what they were doing. In many cases the holes are where the dial will cover then, and you won't even see where it was drilled and repaired.
If the safe has substantial justified damage, then AMSEC should send you a new door. If the damage was caused by the locksmith, he should pay for a new door. In some cases, AMSEC may think it's better to simply replace the safe. If the safe was opened and repaired properly, there's no need to replace anything.
If you would like to e-mail me photos or discuss the situation in private, feel free to PM me. I'm always more than happy to provide whatever assistance I can.