I have a music collection that I've built over many years. As the cost of storage space has fallen, I've moved to re-ripping my CD collection as FLAC format. I've always used the following folder structure when organising my files:

Artist\Album\File

So now I have some Album folders that include both lossy and lossless files. I want to target only these duplicates, rather than duplicates within an Artist folder.

For artists with 'Greatest Hits' albums, I want to retain files in that folder as well as where it appears on the original album. PerfectTunes lists these as duplicates, which I don't want to have to go through and manually de-select for deletion.

Is there a setting that will ensure that only duplicates in the same folder will be flagged for deletion, rather than across the entire music collection?