It could be an issue not related to GNU Boot, but we could still document it somehow as it impacts usability and the goal of GNU Boot is precisely to make it easy enough for users to use it.

For instance if the battery is somehow moved when the undocking happens, it could explain the behavior because  a physical disconnection could happens in some way when the undocking happens.

Another less probable cause could be that the battery is too old so a peek of consumption makes the voltage go to 0, but then I've been using GNU Boot compatible Thinkpads for a while and I didn't see the same battery refusing to charge and then charging again. What I observed is more that at some point the battery decides that it's broken and refuses to charge. And I've not managed to bypass that of find a way to fix the batteries somehow yet (though some people know how to change broken cells while still keeping the battery firmware / chips happy).

Another things that could be worth checking are the nvram settings (things like first_battery), but I guess that they are unlikely to have wrong defaults with reguard to battery charging and so on.

Denis.