Switch SX OS Issue on 0 Percent Battery

Probably auto RCM

 

As @kerelenko said to it's probably in AutoRCM.
1- Charge your battery for at least 30 min.
2- Plug it into your PC.
3- After that you can follow this for Atmosphere Installation.

EDIT: You can disable the AutoRCM with Hekate if you want.

 

It has been about a week. Any updates on the situation?

 

If your Switch has autoRCM, and you do not send a payload, it will just show a black screen when it boots. This black screen is indistinguishable from the Switch just being off. The system will not charge while on this black screen. When you plug in the system to charge it, the system tries to power on. However, since you're not injecting a payload, it just stays on the black screen. Since it can't charge on the black screen, the system does not get charged. The way to fix this is to plug in the system, hold down the power button for a good 10 seconds to turn it off (since it's on the black screen), and wait five minutes for it to charge. Then unplug it from the charger and turn the system on while injecting the payload. Once you have the system actually booted, you can put it back on the charger to let the battery charge the rest of the way.
If it doesn't work the first time, don't panic. You probably just turned the system ON whenever you held the power button instead of OFF. It's impossible to tell whether the system is on or off without injecting the payload. If it won't boot with the payload injected, it means the battery is still dead and to try charging it again. And if you're using something like an SX Pro dongle, make sure the dongle is charged as well (takes less than five seconds to charge it).