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If Calibre does not know about the file, then here is always a danger that it inadvertently gets lost. I think from what you said you are adding this file outside Calibre's functionality so that Calibre does not know about it?
However you should be able to add any file type via the formats section of the Edit Metadata dialog. If you do that then Calibre will know about the file, and will also list it as a 'format' in the Calibre GUI.
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