If I enable to copy non flac files, the program copies over my .sync folder and ruins my btsync share about flac2all HOT 3 CLOSED

Hmm, some sort of input filters for the copy command would be useful. 

I should probably make it work on all input files. 

Thank you, hopefully you'll implement this feature soon, so I can start using 
your program again :)

Ok, revision 61 is the first version that support excluding input files by a 
pattern (standard regular expressions). New switch is added in the program:

  -x EXCLUDE, --exclude=EXCLUDE
                        exclude certain files from processing by PATTERN
                        (regular expressions supported)

In your case, if you add  -x "\.sync" to your command line, it should skip 
everything with ".sync" in the path. 

Please verify and let me know if it works for you, or if you get any errors. 

Thanks!