The problem is that rc2 is for installing on internal memory and you are trying to install it to SD. So instead of installing to SD, it installed it to internal memory and messed up stock.
To fix it, first download one of my plain stock ROM zips from my HD/HD+ CWM thread linked in my signature. See item 6. Then burn a new image for emmc CWM (get it at that same thread) to one of your new SDs and boot to that. It will say the CWM is for stock in the title. Flash that plain stock ROM, followed by a factory reset. Then you should be ok.
If you want to update your SD install, you must pick a ROM zip from the SD thread.
Sent from my Nook HD+ running CM10.1 on emmc.
See my Nook Color Tips Thread here
and my Nook Color EMMC Partition Repair Thread here
and my Nook Color Updated CM SD Installation Instructions here
and my Nook HD/HD+ stock tips thread here
and my Nook HD/HD+ CWM Root Tools thread here