Have you tried manually removing them from your device not within the sync manager?
unremovable playlists in sync manager
I'm a bit of a neat freak and like to have all my music organised with folders and sub playlists but only the playlists that are relevant and needed. When in sync manager, i have 4 playlists that i want to remove from the device however they cannot be ticked or moved, they are not highlighted in white text either its almost like they are locked? someone please help as when i go into my usb when i'm playing i have these dud playlists i do not want!!
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Once again, your answer (Pioneer) prove that Rekordbox is not finished and not enough reliable.
5 years 1/2 later, I have a similar problem (impossible to tick a playlist in order to sync it with a device using the sync manager) unfortunaltely, the playlist tick box is not clickable.