Fortunately for us, both sets of my son's tubes fell out on their own. However, I would think that the removal would be no more uncomfortable and/or painful than the surgery to inplant the tubs. Probably much less painful/uncomfortable. I say this because incisions were made in the ears to place the tubes and the right one will need a small incision to remove it, in your daughter's case. Just remember that there will be holes in the drums and you will need to treat the ears as if they still had tubes and not let any water get in them.
Now, they could be itching and hurting because they are trying to come out. My son said his ears felt weird and "sort of" hurt when his second set of tubes came out. Within a couple of days they both came out. Unfortunately for him, he still has ear troubles and will need a second eardrum replacement surgery.
I hope everything works out well and all the ear trouble is behind yall. Ear infections are the pits. After 10 years of dealing with them, I hate them worse than any other "normal or routine" childhood ailment.
Good luck to you both.