How does the whole transfer process usually work from NAPS to the academy? For example, for a prior enlisted if I only have a certain number of leave days saved up, what would happen when those leave days are used up?
Once you report in to USNA, and you transition from your NAPS status to that of a midshipman, no real leave gets accrued during your 4 years as a mid. You get Thanksgiving, winter and spring breaks in leave status, as well as summer leave periods and some inter-sessional leave days (in between exam end and time to be back at USNA in late spring for either pre-Comm Week activities or start of Block Zero summer schedule. You just...get leave, magically, and there is no counting of it. Once you graduate, and starting from your commissioning date, you once again start accruing leave at the regular monthly rate. USNA grads are also typically given 60 days of "basket leave," again, not counted officially on an LES. Some take less because they are starting TBS, flight school or other pipelines a few weeks after graduation.
At NAPS, I assume you just...get leave during breaks. Nothing official on an LES. What I don't know is if you are able to carry over any leave days from enlisted time to some years later after commissioning - I suspect not. Let's hope some current prior enlisted at USNA or NAPS Post, because this can't be a new issue.