When you right click the Auto-Charger with an armour piece that has a Warding Module to charge it, the item goes into the Auto-Charger correctly, but it will also seem to equip it on your character. The equipping is client side only though, the moment you click the armour piece in disappears again.

Armour with Warding Module:

Put helmet in Auto-Charger:

I suddenly have the helmet equipped, replacing my old helmet:

Clicking on the helmet sets it back to the old one (showing that it is client-side only):

This issue should be fixed in the next release, tentatively v6.0.7. Should you encounter it again, please file a new ticket. Thank you for the report!