Yeah this happens when you save cues in Lexicon to make the results the same as what you see in Lexicon. Because Lexicon only has visible cues, saving them removes the “marker only” property from the cues. When syncing to VDJ, your cues end up as normal cues, the marker only thing is removed.
Maybe the best thing is to restore a VDJ backup, see Backups and how to restore them