Can you opt to select a copy of DSD and highest rate PCM or do you only get the highest rate option with some automated removal ? I know there are many dupes likely so grooming them by hand will be an arduous task.
In all cases SongKong can either delete duplicates or just move them to a specified folder based on the value of When you have duplicate songs
SongKong finds duplicates then decides which one to keep based on the Preferred Deletion Criteria
So by default it will always keep the high-res (24bit) (and dsf) files in preferences to other files because Bit Depth is the first criteria in Preferred Deletion Criteria. If duplicates files have the same value for this then we look at the next criteria which by default is AudioFormat. Audio Format uses the Preferred Audio Format list so we can see that we would prefer dsf, then aif, then wav ectera.