Just caught up on your sitch .... just my gut feel changing the locks will most likely just add to the "Reasons I left you" column. I would think now is the time so start with some boundaries ... your arrangement is a bit different than most as the OM/OC thing was acceptable but now you changed and have grown to have issues with the arrangement, she obviously wants to continue the lifestyle regardless of your change of heart. Changing the locks at this point is just taking your ball and going home.
I would contact her, tell her you have noticed things missing, tell her you would feel more comfortable that she set up a time to remove all her items with you present ... do not talk her out of leaving .. its done, just let her know a good time frame and leave it at that ... then at least if this continues you have set up some ground work .. if she continues to sneak in and take things .. let her know your bo9undary once more and that the locks will be changed to protect your dwelling .. the one she chose to leave.
