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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.