I waffled on whether this belonged in Bugs or Suggestions, but I decided it's a bug since it's clearly not intended behavior. Feel free to move it if you disagree.
The problem is that masterwork bolts (or arrows, in a modded game) are actually less useful than the merely exceptional variety. The reason is that if you use them on an enemy, they'll occasionally get stuck, or drop to the ground unbroken, leaving behind single masterwork bolts.
If even one of these bolts gets melted, destroyed by magma, stolen, or simply carted off by a fleeing attacker with it stuck in their thigh, the bolt-maker will suffer a huge bout of depression, and probably end up tearing your fort apart or killing himself.
Now, if at some point we get the ability to re-stack bolts into a useful quantity (or hold multiple bolt stacks up to N total bolts), I can understand the bolt-maker getting annoyed that you leave his masterworks on the field. However, I get the sense that either of those abilities is at least a few months off, so I propose an interim solution: as soon as a bolt is fired, let the maker stop caring about it. It's already been used for its intended purpose, any additional use would be a bonus.
For the moment, the best I can come up with is to unforbid wooden/bone ones for practice use, dump magma-safe bolts into the volcano, and carefully hoard any remaining bolts deep in your fortress... all of which only makes sense if you happen to be worshiping the Goddess of Ammunition or the God of Packrats.