I’m on the unofficial CM 12.1 build and went back to my stock rom after a full factory reset and it restored fine but when going back to my custom rom backed up by TWRP 2.8.7.0 and restored using newer 3.0 version most of my apps were missing along with my browser website links folder as well. The stock rom I restored was also one from the older TWRP version restored by the newer 3.0 version and it worked fine. This is the first nandroid restore I’ve ever done that didn’t just restore it exactly like I left it and it has me a bit worried.
When I flashed the new TWRP 3.0 and tried to do a current backup it failed saying my system was set to read only. I changed this in TWRP’s settings and the backup worked but I don’t remember this system RW change being an issue with the older version. Are these changes meant for Marshmallow’s more restrictive firmware and just tweaks we will have to make on older lollipop roms ?