Add me to the list of people trying to solve this. After modding my first OLED using the reballing of the eMMC method, had this exact problem with the right joy con not detecting. Haven't seen this problem since so I want to solve this.
I've compared diode readings around the connector and chips on the back with a known good board and didn't find any obvious faults. Last I looked, the enable pin wasn't active when the joy con was inserted. This enable line comes from the SOC unfortunately. Will update this thread if I find anything.
UPDATE: It's now fixed!!! I take no credit and found the solution on another forum by user setryky:
Issue was a cut trace from opening the shield. To fix, I cut away part of the frame and bridged the broken trace and now the right joy con connects with the animation. Hopefully this helps.