Effectively you also say that using this tool usually means losing data.
What would be the disadvantage of rewriting the XML files such that it copies ALL of appdata\roaming? Could this cause any problems? Maybe not the directories which were created by Windows, i.e. Microsoft, Adobe, Media Center Programs, and Identities, but everything else.
How can it be told to copy ALL shortcuts from the Desktop, not just the ones whose targets are reachable while loadstate is running? Currently it omits all shortcuts to server directories. I could mount some of them during loadstate, but not the home directories of all users simultaneously all on the same drive letter, and I do not want to load the user profiles one by one.

