I want reprocessing to work like it did in Nuclear Fuel, not whatever you changed it to!

Set "Reprocessing recipes" to "NF Classic." Alternatively, you can just install Nuclear Fuel and Bluetonium will just work on top of it, like it did in 1.1.

I made an atomic bomb with plutonium but it recycles to uranium-235!

Internally, an item doesn't know anything about the recipe that it came from, so every atomic bomb is going to recycle the same way. If you're using Scrappy Industry, atomic bombs will recycle to radioactive waste instead.

I just upgraded an old save and my advanced centrifuges all disappeared!

Install Advanced Centrifuge and everything will continue to work as you expect.