When she moves out, make the house look like what You want. Change it up to look manly and not her womanly touch. That is often a shock to the W and it helps the H in making the place more like "his" instead of "theirs".......if you want to do that. I agree that you don't need to leave any "holes" where she took something. That would only serve to hurt when you looked at it.
You sound so much better now and I believe you will come through this happy one way or the other. You've grown a lot throughout this ordeal. I am proud of you.
It is not about what you feel should work in your M. It is about doing the work that gets the right results. Do what works!