I just had the weirdest thing happen that I'm not sure how to properly replicate it as I wasn't paying attention. I'll write down what happened to the best I can.
I had just finished Synth Purity Challenge 4/4, reset to do Base Carry 3/6, finished that, went afk for a few minutes, changed the ship weapons and shields around, started Core Computing 7/9 (I was at 6/9 completed), and it immediately completed just as the prestige reset was happening. I was at 6/9, started the challenge with a reset, now at 7/9 at Sector 1.