How about giving us some concrete details. Exactly how do you save the nav file? What steps do you take to try to reopen it? Is there another waypoint file in a pk3 lurking about? Do you have sv_pure set to zero? Have you checked the folder fritzbot/bots/maps to be sure the nav is in there?
It's hard to troubleshoot with so little data. Kinda like telling the auto mechanic "my car sounds funny."