Do they stay the same or does the ability change too? I remember you deactivating being able to receive protean Froakies for some reason. Despite rough skin gible being available before the ability worked, I now aquired an epic froakie with Torrent from Arnie and I am afraid they all will be trash and completly worthless once protean is added so farming him was useless all along?

Pretty sure I already saw some protean froakies around. So the abilities won't change. I think there's a slim chance of the froakie from the reward have its h.a.

their value drops slightly I guess?

You could always get H.A Froakie as far as I know. I've seen many on Blue.