I'm a little confused as to what you think is happening here. They don't take your rested bonus off you. If you switch to a level 50 job to do a dungeon, the bonus disappears as you can't gain any more XP on that job/class. Switch back to a class that isn't 50 - DoW, DoM, DoL, DoH, it doesn't matter - and your bonus will magically return. Nor do you need to log out on a non-50 class to get it; you get it regardless.

If it is somehow disappearing, then it is a bug and you should report it in the bug forum