Is there a way to change a pet that already exists into a Steamworks pet, or can you only make a new one?

There is indeed! That's what I did with [pet not found]. The only difference is that a pet created as steamworks will have a special cog gender, whereas an already-created pet will keep their current gender.

You will need to visit Yun Enterprises with a Yunium Key and the schematic of the species you want. It does not need to match the species your pet currently is.

I'm not sure if the pet has to be your active when you go there or if you get to pick, but it wouldn't hurt to make them active just in case.

Once you follow the instructions and submit your pet to be steamworked, it'll take a couple of days. You will receive an event notice when it is completed!

Oh cool, thanks for all the info! I wanted to be cautious when proceeding with such a precious item as the Yunium Key, haha. One more question, if you happen to know: the pet I want to change is genderless, will that remain?

Yes, their gender will not change, no matter what it is. :)

Thank you so much! :3