Now I'm wondering if I should turn off AutoRCM. I've guessing that's what caused the battery to drain completely. First, should I turn AutoRCM off and if so how do I go back to the hakate menu to do that?
I realize OP is old at this point, but since it was bumped less that a week a ago, I wanted to clarify this for any lurkers with a similar problem in the future:
If you didn't already figure this out...
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 charge 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).
The original post mentioned updating using ChoiDujourNX. If you've done this, DO NOT DISABLE autoRCM! If your system boots a single time without going to RCM and using a custom bootloader, you WILL burn fuses.