Firstly, I noticed that it discharges the battery fairly fast. It was easily 50% after a few months.
Secondly, when the battery goes very low (I haven't determined how low exactly) the battery/power LED starts to blink even when the machine is "turned off" 
It appears that in this state, it discharges itself down to the hard protection in the battery itself, at 2.5V per cell. Job well done 
When I reconnected it yesterday, the battery didn't even want to charge initially, only started on the second or third try.
I have previously stored unpowered x86 laptops with batteries in them for months too and never seen similar problems.
- Li-Ion self discharge rate is very small. At the same time, Li-ion doesn't cope well with full charge. Some Li-Ion manufacturers specify in their datasheets to not store fully charged battery for long term. I've read some smart battery packs for drones will self discharge to about 50% if left 100% charged and unused for too long.
- there's nothing wrong if the LED blinks, the BMS (Battery Management System) will disconnect the battery completely when the voltage goes too low.
- when completely discharged, after the BMS cut out the power, you need to plug the charger and wait. Can take a few minutes until visible charging happens. At first the charging current is very gentle, so to not damage the battery. Plugging and unplugging doesn't help, while you plugged it 3 times, you just complete the time needed to wait. Plug once and let it be. It will start charging by itself, just not immediately.
- older laptops were not so careful with their batteries, but when you need to maximize battery life, like in a Chromebook, then you'll need to apply all the good practices, even when that will make users think you hate their batteries.
