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I'm not 100% sure of some of the terminology you're using here, but unlinking and relinking a database should clear out the local files SQL Source Control keeps. Any differences between your database and your repository should show up as conflicts after a relink. Can you try unlinking, restarting SSMS and then relinking and let me know if that works any better?
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I created a new branch, and unlinked my DB and re-linked to my branch, but the working copy is not changed (I get in "commit changes" changes I've made in the trunk).