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Stored documents are editing externally by UR creating a temporary copy in a subfolder of your TEMP path, and then syncing that file with any changes back into UR. UR won't know anything about a copy you make in an external app via save as. A couple options:
1) Duplicate the document in UR (copy, then Edit | Paste Special | Duplicate), then modify that copy
2) After saving a copy externally, import the file into UR (if you save as in the TEMP path, be sure to import before exiting UR, as it will clean up any files in its TEMP path on exit)
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