Bought a Nicaraguan boa....

[Bogertophis]

... later, I left the mouse on a paper towel in his tank and it was gone this morning. I've heard boas are serious eaters but I'm not seeing that with this guy. Would his age and size have anything to do with that or is he still adjusting to his new home?

As already noted, no paper towels under or near prey. A snake's teeth will catch on the towel & if swallowed along with the meal, they cannot digest it & may not be
able to pass it either.

I think your boa is still too young & in the process of adjusting...be a little more patient about handling etc.- that's all. Fear ruins their appetite.