Official comment
If you've read the rekordbuddy documentation, it highlights this fact. When you make changes within rekordbuddy, the XML file changes, and thus the rekordbox library reloads and requires re-analysis.
You can manually drag-drop tracks into rekordbox, but you lose all of your grid and hot cues by doing so, thus rekordbuddy is a good way to get a highly-customized collection from Serato > rekordbox.