Missing menu 'About>Software Updates' on Stock HTC One M8 Android 5.0.1
Because you have written to the /system partition, it has locked due to the way how updates are installed, they just patch files ie. NO full system image and thus, to prevent bootloops, bricking, malfunction etc., they simply remove the OTA option.

Also: This state is saved and never checked again (because if you have tinkered /system it is intentionally permanent. Restoring /data removes this information and allows a check by the system.

It's similar to how Samsung phones detect if they have been modified; it's not instantly after the installation/reboot, but rather after a few checks (file existence, permissions, sizes, dates, hashsums etc.). This may or may not require some time to finish.

Last note: The availability/existence and extent of those checks may vary depending on the ROM's revision, the model and additional modifications by carriers or the manufacturer itself.