From what I understand, the majority of license and permit fees go towards law enforcement, wildlife research, information and education (outreach), administrative tasks, and acquisitions, among other things, keeping the lights on, etc. Obviously anything left over is saved. The majority of costs pertaining to actual management of the public lands and habitat are covered by Federal Aid Reimbursements, that is, money from Pittman-Robertson and Dingell-Johnson funds, grants, and other partnerships. But in order to fully utilize that Federal Aid, the state has to be able to MATCH it with their own money. Without a match, no fed aid dollars. So if permit and license fee revenue decreases, so does the federal aid reimbursement, as does accessable land and habitat quality.
Here's an article that talks a bit more about P-R and D-J money...
http://www.vindy.com/news/2017/jun/24/conservation-funding-explained/?mobile