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assigning Designator to components autmoaticall through software option is annotation, like (C1, R1 etc) ...
however if you want them to go to their previous original designator you can use back annotation.
If suppose you have done some changes in Layout and would like to transfer those changes to schematics then you can use back annotation option which will update the changes.Generarrly it is used after renaming the refdes in layout,before gerber release.