In regards to charging, the Switch works like this:
- Console charges though USB-C cable and without dock, but joy-cons don't.
- Battery-drained joy-cons not charged in the dock will work only if attached to the charged console, as they will use console's battery to work as a portable, but won't work unattached from the console without being charged in the dock with console or on a dedicated joy-con charger.
If you haven't tried this yet, just charge the console in the dock with the joy-cons attached in order to also charge the joy-cons or use a dedicated joy-con charger as an alternative.
Not sure if this is the solution for your problem, but I hope it makes sense and helps you somehow.
