I remember soon after the Bestiary was implemented, I completely unlocked the Young Troll entry which was removed from the Bestiary two weeks later. I kept the extra 15 charm points for a few days/weeks till it was fixed on a patch. I believe that since this patch, the server periodically checks the unlocked entries and updates the amount of charm points characters are supposed to have.
I'm not aware of anyone being in the edge case of having less charm points than what will be subtracted due to creatures that have been unlocked being removed from the Bestiary. However, I do expect it to be similar to Tibia Coins counter in case of payment reversal, i.e the counter becomes negative and further "points" can't be exchanged till enough points are obtained and the counter becomes positive again.