kme,

David is right -- talk to your doctors and ask if it's okay to stop for a while. I, too, am in the middle of radiation treatment (16 done, 14 to go) and the fluoride trays sting horribly on my top teeth. My prosthodontist told me not to worry about stopping if it is so irritating, and to resume when it doesn't hurt so much (presumably after radiation is over). But ask your doctors first.

According to my prosthodontist, the weeks following radiation are the crucial ones to really start using the fluoride trays.