Could one deepfake one puppet onto another?
I’m not sure if deepfake software works on non-human faces, I don’t think so (but if it does, it could be a good solution). But something I’ve been thinking about trying (other than just manually animating and overlaying an improved face in After Effects) is using the free EbSynth software https://ebsynth.com/ which can replace the texture of a moving shot using keyframes as a guide. So what you would do is to create a few keyframes in Photoshop where Yoda looks how you want him to look, and then the software will try to make the rest of the frames match that look. It might work.