The ESC brake and BEC functions do not have any direct relationship so ideally using the brake doesn't affect the BEC output in any way.

There's an indirect relationship though: If using the brake heats the ESC up a lot, the BEC circuits will heat up as well and it's output power may drop as a result. That said, if you monitor the ESC temperature and it doesn't become hot, there shouldn't be any problems with the BEC function either.