The battery should still charge while in RCM mode, but it won't have the software necessary for fast-charging.
I would first, fully turn off the switch or enter into RCM and put your switch on the charger... Eventually, the battery will charge enough and you can connect the Switch to a PC. You can use the TegraGUI app to push a payload and wake up the switch without your dongle.
Also, go find your dongle!