For future updates to ensure you have all the files required you can upload the main zip file that comes with each major release. For example: https://github.com/Duet3D/RepRapFirmware/releases/download/3.1.1/Duet2and3Firmware-3.1.1.zip
Upload the entire zip file as is to the system tab in DWC, and it will take care of the rest.