They are removed once used (and, like all combat markers assigned to armies, must be used if the assigned army is designated for combat and applicable (i.e. a defense only bonus is not applicable if the unit attacks)).
The only markers that remain for the entire game (unless the assigned unit is eliminated, as described on the card) are Elite Mountain Division and Allenby. The Inspired Leadership markers and von Straussenberg marker might remain if the conditions listed on the card are satisfied.
Thanks again for the quick reply Kirk. I thought so but wanted to be sure.
In my opinion, you've got a winner here.