When deactivating tomes, any effect that you have purchased will remain. Is this expected behavior? The game makes it sound like deactivating the tome removes those options but they remain during encounters.

No, deactivating a tome doesn't replace any active transformations. Were you expecting that it would undo it to the previous body part?

If you're wanting to get rid of an infestation there are uninfested parts in the anal tome, genital swapping tome, phallus tome and vagina tome.

When the box pops up after clicking hide and says "deactivate effects of this tome?" I did initially think that it would make it as if you had never used it. I did find the pristine parts through the other tomes though, Thanks!