Talk about bizarre! I ROMmed my son't Nexus with the exact same sequence I used: TiBU, nandroid, superwipe, JBSourcery 4.1, Gapps 12/12, reboot. And TiBU only showed ONE APP to restore!
Lacking everything but ingenuity (
), I went back into TWRP and did a partial nandroid restore of the /DATA partition only. Best case? He gets the latest ROM and all his data back. Worst case, the phone borks and I have to start wayyyy back from scratch with the Toolkit.
It WORKED!
One happy son now
Disclaimer: YMMV