Ok, got this issue for the second time (Owning a pre3 from September, and the battery health is at 93%).
Off touchstone for an half hour, then after closing all the apps I was running and after pressing the power button to make it lock, the screen remained on (but not responding to touch).
After some seconds I got the Low Battery message, and after some minutes I put it back on the touchstone.
Well, it slowly began to charge, until it got 21% (well, the battery was near 80% when the issue occoured).
What I think is: the A6 got mad and thought the battery was 0%. It began to charge, but when reaching 21% the battery blocked it (which should be a good thing, prevents overcharge).
So I needed to fully discharge it (was sticking to 0% for about 5 hours... lol) and now is recharging.
So, if someone else is having this issue: DO NOT shutdown or reboot the phone when the Low Battery message appears. Otherwise the "low battery" icon will show at next boot, and that just makes all the process longer. Just wait until it discharges completely, then begin to recharge it. Or, just use the phone normally, but it may shutdown on you without advice!