Custom D.E.O.T. V2.0+/Clockwork OS v0.5 image - With customised DEOT interface, Kernel 5.7, Optional 1400MHz OC, Debian 10 Buster, Retroarch 1.9.0, Mupen64+ plus more! (Current build: 200903)

I have had this exact problem before, and basically did what I mentioned re unplugging for long periods.

Check out this thread. Sounds like a similar problem to yours.

A thought.
It only really charges when the logic board tells it to. Use the old image that works to fully charge your battery perhaps.

It’s strange that it’s only the new image that is affecting things.
Just try this for now. Replace the contents of the boot partition with the files in the kernel.zip here. That’s the only thing I can think about.