I have had an old reclaimed pine floor sanded and stained/sealed with bona stain and traffic topcoat. After sanding, the contractor finished staining and there were some color differences between areas that were of different origin. I applied a darker pigmented bona stain to the areas that were lighter, and it appeared to be relatively uniform in color. When the topcoat of bona traffic was applied to the whole floor, the double stained section was very rich looking and had good sheen. The remaining section had a lot of white blush and the finish appeared not of consistent sheen. The white blush did mostly disappear, but the finish is nowhere near as nice as where the double stain/seal was applied. I want to darken some areas and then put another coat or two of traffic on.
Can I sand the finish aggressively almost to the stain and use a stain(not Bona stain/sealer) to achieve the color desired and then use shellac and then the traffic. Or what do you recommend. Thank you in advance.

No, once a coat of finish is applied, the stain has nothing to absorb into.

I have heard of tinting the finish, but being a chemist, is all experience and luck.