How do I prevent duplicates from multiple file types. I.E flac and mp3

[JusieBoi 0]

How do I prevent duplicates from multiple file types.  I.E flac and mp3?  
Do I delete from the streamed folders?  I would prefer not to delete any files.  Is there a setting to allow one of each file based on preferential file type?  I.E flac?
I have a program called winmerge that will compare all the paths I am syncing to emby from.  It lets me know where the duplicates come from, is it best if the above is not possible, to use this to isolate duplicates and delete from my streamed folders? 

Any advice would be helpful
Thanks