Hello, Eric.

Thank you for contacting us.  After you have moved a bookmark, or made other changes, in Smarky, you should immediately export the changes to Safari by clicking in the menu: File > Export to Safari.  Then the changes will "stick".

But, hmmm, Smarky should remind you of this when you quit.  This leads me to believe that maybe you are leaving Smarky running all of the time, which wastes system resources and is unnecessary.  Normal usage is to switch on Syncing and then leave Smarky quit except for when you want to do major bookmarks housekeeping.  Sorting/Syncing will happen when Smarky is quit.