Well. ..
If you have stock recovery. ..you could go into your super user app and remove root. If you need stock recovery run CF Auto root then remove SU within the super user application.
Then attempt the OTA update. .( may not work due too tripped flash counter anyway)...
If it works or not, run CF auto root to get your root back.
But you would need to flash your alternative recovery again once the attempt is done if you want a custom recovery.
Long shots yes, but the OTA interface "WILL" check for a modified binary most likely.
Just thinking out loud...g