This is a very good question, have you tried bootable partition software to see if you can format it, maybe it is a partition that Windows is not able to see.
I'm not sure what happened, but after a couple of reboots, it now shows up in Windows. It shows the drive as offline, but it's there.
I'll call this one answered.
Thanks as always Ivan. I tried to remember what it was I did between the eMMC not being there and it showing up. The only thing I can think of is that I booted it into Linux from a USB. Not sure why that would matter. I was able to set the eMMC online and it seems fully functional as a second drive now.
I'm considering wiping it and using it to boot Openelec.