Normally, uploading a new file for an existing product would replace any old file previously uploaded to that product, so from that point onward, all unexpired or reactivated download links previously issued for that product would download the new file.
However, if you were using PDF Stamping for that product when the affected buyers made their original purchase, their original download link would always download their original Stamped copy, even if you reactivate their link. This is explained on our PDF Stamping help page. To issue these buyers a replacement link for an updated file, you can use "Send free download link" in your Seller Admin, which would also apply any PDF Stamping you may currently have set up for that product.