Remove scanned highlights from a scanned document

You would have the best control over adjusting the color in Photoshop, but it may be possible to do in Acrobat using a Preflight Fixup. (Tools> Print Production> Preflight> Fixups) This works well for changing the color of vector objects, I have not used it very often for images, but if you have many scans to change, it might prove useful. Find the profile Map color with specified color values and duplicate it, you can't edit the original profile, which is why you need to duplicate it from the little fly-out menu. Set the Source color value to match the color of the highlight, set the Destination color value to the background color, set Apply to: to All images, click OK.

Acrobat cannot remove scanned highlights. You could, on a page-by-page basis, open it in Photoshop and use the color correction tools to remove the yellow highlight, but that's not something Acrobat can do.