My suggestion is to select the two book records of different format, and do as follows,
- Edit metadata
- Merge book records,
- Merge only format into first selected book - delete others
Or for short cut, select the two book records with different format, "ALT SHIFT M"
BTW, I've read in previous version Calibre used this option for merging them,
Turn on the autosort/automerge option located at
Preferences|Add/Save|"If books with similar author and title found
It will cause Calibre to identify the second book by author and title,
determine if there is another matching book with that author/title and
then add the new format to the existing matching record.
My version is calibre 0.8.38