They should not ever take things from your sight, nor inspect them without your explicit approval.

You probably can't remove the residue satisfactorly.

I do know of a case where the TSA confiscated the shoes of an executive from my former employer. He owns a farm. He had walked through freshly fertilized areas. It set off the trace detector. TSA refused to let him take the shoes on board, no way no how. And no amount of explaining, x-rays, or anything else convinced them otherwise (they were dress shoes...).

He showed up at the arrival airport with no shoes at all - our meeting planners had to find a shoe store for him.

He promptly called the airline, canceled the return flight, and (after the meeting) took a rental car and drove home 1200 miles. I do not believe that he's flown since.