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We're not aware of any way for UR to discard external changes made to a stored document (that doesn't mean it's impossible, but we have tested it quite a bit and verified that it works properly in our tests).
You don't actually have to do Ctrl+S in UR -- if not done already (due to auto-save, File | Save / Ctrl+S, or Tools | Save All External Documents), before the database is closed or UR is exited, it will sync all UR item(s) with any changes to temporary file(s) for the stored document(s).
One way you can verify that UR has updated its stored document from a modified external copy is, after saving in the external app, select the item in UR (if not already), do Ctrl+S (or File | Save), then File | Export and export as document to an empty folder, and open that file in the external app to verify the changes are there. If they're not, with UR still running and that item selected, choose Item | Open Containing Folder to open the folder with the temporary document being edited externally, and copy it somewhere and/or verify that it has the changes.
If you do find a scenario where UR doesn't update its stored copy of an externally modified document, please send as much detail as possible for us to reproduce the problem. Thanks.
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