Hi dpaanlka, I got the same effect with my crates and the sync manager: the track count on the destination drive was always somewhat smaller than on the source EP drive. I decided to take some time to investigate which files were affected and found out the following:
I had a few cases where I (accidentally) had duplicates of the same track file in different subcrates. As the duplicates have been in different subcrates they were obviously hard to recognize. From my understanding the following happens: While using the sync manager, it iterates through your selected crates and starts to copy the related track files into the file structure on your destination. However, when sync manager gets to the subcrate on the source that contains the duplicate, i.e. a track file that it already finds on the destination (because it was already copied), it does not copy it again (or overwrites the first instance - I’m not sure). And this is exactly the reason why you have a smaller number of destination files: because your source crates somewhere contain duplicates. If you copy the files manually, the duplicates are of course copied also, so no difference between source and destination.
So, somewhere in your “Sorted” (sub)crates on your source you will have one duplicate file - I bet . On my Windows laptop, I used Mp3Tag to spot the duplicate by sorting all involved track files of the underlying directory.