I have checked on the ticket that was opened in the thread that you linked to. I suggested a test of removing the files from the server after an evening of editing to see if the issue occurred for them when the files were not present. There was never a response to my post.
There is nothing in the db or the scripts that would be automatically removing these options for you. Only if the server behaviors that remove these options are triggered should the options be removed. It looks as though you are still working on this with Jason, I would suggest that you continue to work with Jason to find resolution on this issue. I have also sent him a message about the other thread and ticket that was opened for it as well.