In the latest commit, specifically commit number 0df9e35, when answering Yes to the Save to PKHeX's database prompt it in addition to the Pokemon in your P.C. boxes it will for some reason also add some blank .pk6 files to the db folder.
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Seeing as I have already made this thread I may as well ask here. Speaking of the PK6 Database, as a feature request would it be possible to add a search filter to choose between the Pokemon in your P.C. boxes and the Pokemon in the PK6 Database?