I don't know about Atlantis, but testing with MS Word, LibreOffice, and WordPad, via Item | Show Explorer Menu -> Open With, editing the document, then saving via Ctrl+S, exiting and returning to UR and clicking 'Click here to resume internal editing' or Item | Edit Internally (Ctrl+Shift+0), always shows the edits from the external application. Make sure you have the file extension of the file you're editing added to 'Tools | Options | Documents | File extensions to open stored documents writeable' checked so that it can be saved.
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