Does anyone know what happens when I zap/give an elixir to/do a merana quest on a pet that has a custom overlay?

I adopted a pet from the pound who has a custom overlay. (I have received permission from the original owner to keep her as a custom). She was originally hydrus, but because she was in the pound she became common again. I want to change her back to a hydrus, but I'm afraid that if I do that, I might lose the custom overlay. But I would love for her to be "the custom hydrus serpenth" instead of "custom common serpenth".

It shouldn't affect anything, and if you did get the overlay (as in, you were supposed to and it's not a glitch that the overlay transfers with the pet) then you should be able to reassign it from the custom overlay page even if it is affected.