Okay so I totally had a panic attack earlier after letting a pet go into the Rift, and he did come back, but since I didn't know about the species that could actually be riftborn, he came back as an RA-001.
My question is... Is there any way to turn him back into a Keeto or am I just screwed? This whole thing is really messing me up and I'm legit devastated by my own stupidity.
[egg=angerandagony] [tp=angerandagony]
Don't worry! You can totally change him back by using any of the Keeto Elixirs. The cheapest one currently on the shop search is at about 38k right now.

You can change the species and color of your pet with an elixir. [Item=Common Keeto Elixir] will turn him into a common Keeto, for example. Any "Potion" will change the color of your pet without changing its species.
The elixirs come in many of the "normal" colors - dawn, dusk, sun, twilight, golden, marsh, arid, etc.
[Url=https://www.subetalodge.us/pets] Subetalodge is a good resource for pets/colors[/url]
Also just a warning, the Zapper located in the Darkside has a chance of changing the color or species of your pet!