Ah okay, than it's not the 64bit cap. Was my first idea that would explain a flip into the negatives.
I've just let the game run idle in the background and suddenly the atoms where negative.
I was able to presige using super humans but that's not a long-term solution because of the increasing requirements for a super human.
Maybe an "quick-fix" would be to add a button that sets the atoms back to 0.
I'll try to see why it flips to negative numbers now that I have positives again.
Okay, from what I know, it always happen when you leave the game generating afk, so, for every other people that saw this, they don't know what's happening, and that's difficult to track the bug. Also, the Prestige dissapears because it unlocks at 1Oc, and a negative number is lower than that, so it dissapears lol