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

Set "Reprocessing recipes" to "NF Classic."

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. The only way I could get around this would be to add a separate "plutonium atomic bomb," which seems like it would be more inconvenient most of the time.

I just upgraded to 2.2.0 and my advanced centrifuges all disappeared!

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