See comments in AAC here: https://answers.atlassian.com/questions/158312/sourcetree-fails-to-open-repository-after-converting-it-from-hg-git

Presumed browser.plist not updating when reloading - best way to fix would be to manually edit the browser.plist file although not preferential. This also seems to permanently affect the submodules of a repo even if you've removed and re-added the bookmark.