I know this question was asked a good many years ago, but I found it just now and decided to comment for the next viewers. I hardly use my joy cons, preferring to dock with a pro controller, I had left both joycons in the original grip to float around the house till I needed them again. Only to find that the right would register, but not charge. My first thought was the rail … and I bought a new rail. I took the left battery to try it in the right, and I found it wasn't an issue of both rails. I then took the right battery and placed it in the left controller … yeah, I need a new battery. Plus side of the new rail, it doesn't release as easily as my white box original rail did, I'll be keeping it. Btw, batteries are easy to change with a pair of pinpoint tweezers. You may want to connect the terminal before putting the battery in its place if the wires are not twisted for it's appropriate side already. Just make sure you don't try to connect it backwards, if it is not an easy fit, try the other side.
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I was having an issue with the left joycon not charging and eventually the battery died due to this. I was going to buy a new battery and install it myself. But to make sure that was the problem my plan was to swap the bad battery with the good one in the right joycon. When I opened up the left joycon I noticed the battery cable had come unplugged so I just plugged it back in. It was a little tedious to do since everything is so tiny but once I got it plugged back in it worked fine, no issues.
Just thought I'd let everyone know in case the same happens to someone else
von Jacob Seibel