Your backup should work fine, I was on CM11 but decided to go back to stock yesterday. I restored my TA backup from 4.2.2. Effectively soft bricking the phone while relocking the phone and restoring my DRM keys, then immediately used flashtool to flash the global 4.4 update. All worked fine. On first boot it updated my NFC firmware which I believe is TA linked but its running perfectly now.
Sony Xperia Z1