Basically, I keep two(2) library's. One for FLAC files and another for mp3 files. The FLAC library is for critical listening and the mp3 library is primarily for mobile devices. I use PerfectTUNES on the FLAC library to fix artwork, tags etc. In general the album's in the FLAC library are whole, meaning all tracks.

I also use PerfectTUNES on the mp3 library to eliminate duplicates after the FLAC's are encoded to mp3. An example would be when I have a "Best Of" album in addition to other albums by the same artist. For mobile devices I use de-dup to delete one track from the "Best Of" to save space.

The problem is PerfectTUNES shows the FLAC and mp3 versions as a duplicate. My library is comprised of about 10k tracks.

Question: Is thewre a way to save the PerfectTUNES scan's of my library's separately or a configuration to include filename extension as part of the comparsion?