He is right, as here is the forum for the "Find Duplicates" plugin what just make something totally different of the probem you have.
Anyway, First I do not understand, why you're converting the RTF-file with libre office, just open it with Office 2003/2010 as they both can read it. There you can work with them and then save them as RTF (to come back into Calibre) and DOCX.
The reason why Calibre doesn't add the file to the existing book can be various.
- The name of the file and the import settings could be the way that Calibre doesn't see them as one book. Rename the file, change the import settings or merge them with the merge function of Calibre after you deleted the old file versions.
- Your import settings could say on import automerge and drop existing file formats, that's just the setting I use. Delete the old format in Calibre and reimport afterwards.
- Your import settings say don't automerge, but then you should get a question if the book should be imported as a new version. Just delete the old file versions and merge them with the Calibre marge function.