1) On a one of kind collectable with significant provenance, glassing the head could hurt value to some folks.
2) If not refinished correctly and/or over sanded.
3) Any time a gun is disassembled/reassembled, there's a small risk of damage ie stuck screws/wood etc.
4) When you ship a stock/gun to get work done, it could get damaged/lost.
That's all I can think of right off hand. In 99% of guns that are shooters, it is the right move despite small amount risk IMHO, especially if there are any cracks externally/internally.