To do this in bulk, I'd do the following:
1) ' Embed Metadata' on all books
Do not automerge books on adding.
Read metdadata from file contents. (both are on the 'Adding Books' settings)
2) Create a new library
3) Do an 'Add Books' from your original library *directory* into the new library, using 'Add books from directories, including subdirectories, multiple books per directory'
That should get you a book entry per format with the right metadata in your new library. Figuring out which format is which and doing something with that is left as an exercise for the reader
