Bob you may also want to clean the glass surface on your lapping film paddles, (or what ever type of paddle you are using with the films) before applying a new piece of lapping film, and clean your hands first also, to prevent cross contamination. I have had a piece of some sort of contaminating particle get stuck between the film and the glass right in the middle of the trail the film follows up across the knife metal. With every stroke, I felt the bump, rendering that piece of film useless. After removing that piece of film cleaning my glass and hands, and replacing the film all was fine again.
To answer your specific question, like TC suggested , I too do clean my used lapping films with Isopropyl Rubbing Alcohol applied to a soft towel in between film grit changes while using them in a normal sharpening progression.
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