I am really confused with this Joycon issue… I double checked continuity from rail though to the small 5 pin chip, and it all looks ok. I swapped out the 5 pin chip, just in case. I have already swapped out the PU chip on the back. Still nothing.
I will continue to dig, I guess next up are the 6 pin chip on the back (that bigger one, not PU)…
Pretty sure the fan shares the same rail as joycons, so if the fan comes on then the rail is likely present (?) you could also measure the voltage and check too.
What are the symptoms, is it that the joyconn simply doesn’t charger but button imputs work otherwisee? are you getting the snap animation when connecting it? there are line/s dedicated for detection of the joycon and without it you won’t get the snap animation, I don’t remember if they’ll charge without that line, there is also current sense line/s if I remember right too- I would buzz out the pins on the connector to the opposing side of the board (fuel gauge side and area) on a known good board and draw up a continuity map a bit like my one for the otherside, last time I repaired one I had to run 3/4 jumpers going around the board due to via damage.
Symptoms are that there is no Joycon detection animation, as well as no button presses. I dont know for sure about charging as of yet. I have confirmed continuity from the connector to the 5 pin nearby, and to the PU chip on the other side.
I still need to check for continuity though to the 6pin chip on the other side, as some of the connections go there, there are also some that go straight to the APU, which could be an issue…
One quick and dirty way of seeing if something is open is to just take diode/resistance measurments relative to ground at the joycon connector in both probe polarities and compare to a known good, if a line is open there is a chance you’ll see it, bit quicker than making up a continuity map though this is not a foolproof method as there may be lines your meter can’t get a reading on etc
There are 3 lines that have different readings, but none that are OL when they shouldn’t be or anything.
How different are the readings?
I’d probably buzz out where those lines go on a known good and see where they’re headed 
I worked it out! I’m such an idiot 
You remember right near the beginning I said this area of the board went swimming during the BQ swap? Well, it looks like I may have put the 6 pin on backwards. I swapped it for a spare and it is back up. The text on the original was almost gone, so its hard to tell, but I think it was backwards!
Either way, Joycon now detected!
Thanks for all the help!
Haha easy done. Glad you got it all back up and running 