The files would not be duplicates as they would have different extensions.
I would filter for MP3 files,
rename their folder so that the FLAC files and MP3 files end up in the same folder.
Now filter for flac files and rename the folder again so that all files in the folder are moved to the new folder, e.g. d:\my music\ALBUMARTIST\YEAR - ALBUM_allfiles
This should leave all folders untouched that contain only MP3 files.
Now filter for the MP3 files again where
NOT %_DIRECTORY% HAS FLAC AND %_EXTENSION% IS MP3
this should show all MP3 files that have been moved along with the flac files which means that there are already flac files for that album.
These files could be deleted.
Now filter for the extension MP3 again and rename the folders back to your original naming scheme and do the same for the flac files.
To rename a folder, use Converter>Tag-Tag for _DIRECTORY and enter a full path like
d:\my music\%ALBUMARTIST%\%YEAR% - %ALBUM% (%_extension%)
do not add the filename part.