Update, I did end up losing only data, so thinking back what could have caused it, the last thing I did was install SuperSu, but removing that did not fix it, I ended up removing Xposed, and that is what fixed it for me. :victory:
I have been running CM12 for a while now on Verizon Note II. Tried a GSM Sim card and sure enough no incoming calls and unable to hang up. I tried newest nightlies and still no dice.
I tried modifying the other rom mentioned here but install fails with TWRP. I think TWRP is probably the culprit here.
Edit: installed CWM and still no luck. It says the zip file is bad. Could someone PM me with a link to a zip file of a nightly ROM they know works please?