This suggests to me that you most likely have an arrayformula in the attached Google Sheet?
Perhaps that’s used to flag your duplicates?
If that’s the case, my suggestion would be to get rid of it and instead build that logic in Glide.
It won’t solve the empty row issue in your GSheet, but it should prevent new RowIDs being added to those empty rows. Which may in turn solve the bigger issue.
That said, there have been reports recently of weird stuff going on with Google Sheet syncing. See below: