I guess so, but, the system has to assume that the album title you have in the library is the one you want, so, if you did want to keep the duplicates you could differentiate in some way

e.g. ALBUM A (MP3) and ALBUM A (FLAC)

That it stores by album title is pretty standard with most ripping and storing solutions.

Anyhow, export and restore are features of the wishlist thread so we can make recomendations there.

Rgds,
Nick