Success. We were able to make a recording tonight of both the Main Outputs and the Line Inputs.
We tried a bunch of things, including deleting folders on the PC, re-formatting the SD card, and nothing helped. The SD card wasn't being recognized by the M20d.
The fix for us was to create a brand new Setup from scratch. I then added all of the instruments and microphones to the Stage again, did the usual auto trim. After we did this, the SD card was recognized, and the recording was successful.
I have updated my support ticket with the steps that i went through. Maybe someone smarter than me will chime and tell us what's going on. All I can suggest is to try creating a new setup from scratch, if you are having problems with the M20d recognizing your SD card, or if your recordings are not working correctly.