I had a Integrated Dynamics battery with some charge in it, and an Integrated Dynamics network linked up to some Sophisticated Storage chests. When I put the battery inside the network through the storage terminal, it stacked together with an empty battery and that cleared the battery's power level. This happened once by accident and later I reproduced it on purpose a second time.
I'll come back with some more information soon, I want to test if it does the same when I put the battery in the chest directly vs. going through the storage terminal.

And actually does it happen with hopper piping the battery in as well? It may be that the item's unique id for some reason matches the uncharged one even though I would find that odd.

Okay, I confirmed that this is an Integrated Dynamics issue since I was able to reproduce it with a regular Minecraft chest.