Well, the over the air updates (aka OTA), they are always very particular about any system modification. Whether it be root, or a custom recovery, etc., pretty much any system modification will cause those updates to fail. Now, if you want to update your phone, most likely your only option will be to reload the factory image (which will most likely wipe EVERYTHING from the phone). Once that is all loaded and booted up, you should be able to take the update.
