How to unload filament without cancelling print
This condition is covered in the MMU2S manual's section on troubleshooting:

13.4 All five LEDs blinking red and green
MMU2S unit can now deal with a state in which the Trinamic drivers were not able to provide enough power for steppers. A possible cause can be a broken MMU2S power supply wiring, connectors etc. Please check that all connectors are properly plugged into the MMU2S board and make sure that the cables are in good condition. Also, make sure that the screws on the Einsy terminal box for the power cables are properly tightened. If this state is detected, the MMU2S unit rehomes and automatically continues printing. If the problem occurs three times in a row, the MMU2S unit stops printing and starts flashing continuously with red and green LEDs. Printing can be restored by restarting MMU2S unit using the button on the right side of MMU2S unit.

So, once you have fixed the problem which prevented the filament from moving, press the reset button on the MMU2S. It is recessed, so you will need a tool to push it (such as the 2.5 mm Allen key included with the printer). You will then need to wait a few seconds for the MMU2 to complete its reboot and be ready to communicate, before telling the printer to continue.
Note that the filament may have been chewed by the MMU2 or extruder drive gears and unable to feed properly. Be prepared to — if you haven't already — disassemble the tubing and manually pull out the remaining filament sections. I find this modified holder for the MMU2's filament tubes that uses push-in couplings instead of a clamp very useful to allow quick access when there's a problem or even when inserting new filament.