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Storing multiple versions of the same format is not supported and Calibre is quite likely to end up removing one of them. The Calibre metadata database will only be tracking on of these files. Normally ending up with multiple files (with slightly different versions) is normally a sign of something going wrong at some time in the past.
You can detect which files are not in the Calibre database by running the Database Maintenance function.
The only reliable way to handle such cases is to store them as a different format (e.g. As part of a .rar archive or a .7z file, or to have multiple database entries for the same book (typically including something in the title to differentiate the instances).
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