The maker of Hekate suggested this :
https://github.com/CTCaer/battery_desync_fix_nx
Yes, that is very likely because of the missing chip. That is a safety measure Nintendo added to prevent the Switch from catching fire.
In many cases it is a problem with one or more solder balls of the emmc not making contact with the PCB anymore.
Unless you have some (deep) scratches somewhere on the PCB.
If you are planning on using an emummc, then you can just leave it like that.
The emmc will be 8 times as slow but since it will only be used during the boot you won't notice it.
Only when preparing the emummc you have to wait 8 times as long.
The emummc runs off the SD card anyway and not impacted by this issue.
Reflowing sometimes solves it but it depends on how bad the situation is under the emmc.
If you haven't done any reflowing/reballing, don't try it on a Switch the first time.
For reflowing 420C might be a bit too hot imho.
Those are temperatures for quickly removing the chip after 10~15 seconds after preheating at 200C for 1~2 minutes.
But a lot depends on the equipment you have.
Again, leave this stuff to someone who has experience with that.
It would be a waste to ruin your Switch.