Paxchristos, I have not yet got to these files, yet, but I will. I can say one thing for sure, as the old saying goes, you can not have the cake and the ice cream at the same time.
More I think about this, and doing a cross reference on the files, which will take some time, for some dume reason, I think the root is holding on to some files, like glue and, I would venture to say you are actually deleting some of those files when you unroot. The second side of this could be when you delete the bloatware (as they call it) you might just might possible be deleteing some files that the update is looking for, and thus the update fails. It is a long shot, but I will check this. Don't hold your breath, this is going to take awhile.