ok, I understand. I do realize that you have thought the temp file approach through very thoroughly. It is very clever. I do have a couple of additional thoughts:
1. For a doc that is both stored and linked, since Synchronize overwrites the stored version with the linked version, one has to be very careful not to edit the stored copy thinking that the changes will be preserved since they may be overwritten if synchronized. Maybe your prompt warning should occur when opening a stored document that is also linked (ie, "Warning: any edits may be lost after synchronization"), rather than when UR tries to upated the stored document from the temp file. Or better yet, if synchronization allowed the stored version to overwrite the linked version if it is newer (I realize that poses problems if both versions have changed).
2. I have one particular (albeit obscure) program that I use that, when I open a stored document, the program is unable to save to the UR Copy that is created. When I click Save, I get a Save As dialog. If I then navigate to the UR temp directory and try to save the file over the existing UR Copy in the temp directory, I get an Access Denied error.
In case you wanted to try this yourself, the program is a free music editor called Power Tab Editor (v1.7) and can be found here:
http://www.power-tab.net/downloads.php
This doesn't occur in this program if I open a file directly from Windows Explorer.