You need to swap soc & emmc because soc has (unique) keys for the data on the emmc and emmc has (unique) data for the soc, rest should be no issue
It seems to be a problem with the soc. I disoldered the soc from a donor board and found the corresponding pad under it… so the false switched enable signal for charging the right Joy-Con comes direct from the Tegra X1…
and my skills are not good enough for changing a soc. 
Have you tried using a resistor to force the signal to be high/low?
Could be a workaround but i don’t expect the charging symbol to appear in the controller menu