The charge controller’s idea of what’s going on is totally independent of what’s going on in the CPU. It doesn’t know and doesn’t care about your OS.

Multiple calibration cycles are pointless. Doing it once (every few months) should be enough. Or doing it never is fine too. I had one laptop (thinkpad l480) that would get out of calibration, such that the charge controller would go straight from 45% charge to 1%.

What’s happening is that lithium batteries have a very steady voltage for most of their usage. The voltage mostly changes at the top and bottom ~%10 of charge. Everything else in the middle is guesswork - the charge controller has to measure and count every drop of current going in and out of the battery. Measuring consists of a current meter - you put a very low value resistor in line and measure microvolts of drop across it. You can have a high precision current meter, or you can have one that “doesn’t burn a lot of power in the dropper resistor”, not both. Some systems have too inaccurate a meter. Some have phantom draws that aren’t well accounted for (like the battery’s own internal resistance and drain). If the battery spends all of its time in the “voltage never changes” region, the current counter’s guess will diverge from reality.

When you discharge/recharge the battery, you are forcing its current counter to realign itself with reality. Whatever it thinks is left in the battery, nope that’s really zero when we drop to ~3.2 volts.