I had the exact same problem (changed the shell, left and only left joy con didn’t charge but still worked while docked), and when I went to my local game shop they docked my left joy con to a different switch console. The battery indicator said it was fully charged, and when I docked my left joy con back on my console, the battery indicator was working, and it was fully charged. You can also try updating the joy con firmware under settings, which I did as soon as I got home, and haven’t had problems since.
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Hopefully this helps anyone in the future with this problem.
I had the exact same problem (changed the shell, left and only left joy con didn’t charge but still worked while docked), and when I went to my local game shop they docked my left joy con to a different switch console. The battery indicator said it was fully charged, and when I docked my left joy con back on my console, the battery indicator was working, and it was fully charged. You can also try updating the joy con firmware under settings, which I did as soon as I got home, and haven’t had problems since.