This morning, I did a backup of my GN2 (LJC). Was planning on going to 5MA rom and firmware. Before flashing 5MA, I realized I didnt' TB those apps. Went to reboot back into the system, and got an error there was no OS. I didn't try rebooting into recovery; I didn't think of it at the time. So I flashed the 5MA. I figured I could just restore it later. Installed 5MA no problems. Did a nandroid for the 5MA to a working state before I start adding more mods and tweaks.
Before going that, I figure I would do a restore to the LJC. Went to restore, and only listed the 5MA backup. Check on the PC using file explorer and can see the backup for LJC. I did see the LJC only has seven files and the 5MA one has nine. I went into TB and asked it pull from a nandroid, and did list the LJC. It's analysis found no apps. This wouldn't have solved my problem in the end though.
I tried to search to see if anyone had a similar issue, but no luck. I did remind about the TB nandroid thing though. I think TWRP didn't do a correct backup of the LJC, and that's why it's not being listed.