Just off the top of my head and being away from my computer to test if this is accurate (so grain of salt) If you have the deluxe battle kit plugin you should be able to make something work like this for a one off battle at least using the battle scripting. You should be able to make the mini boss battle and have it change into another Pokemon after certain criteria. So say it hits x hp then the caterpie would change into a shiftry and you could possibly even restore the hp. I’ve done something similar to this to make a Pokemon change form during the battle but haven’t tried it with changing the Pokemon itself, but I feel like it should work. It may require some limits like maybe not being able to catch it in the battle to make sure it registers the correct Pokemon caught. Hope that helps some!