i've done it many ways:
* put a piece of white trans film over the reg. marks and hand-draw them back on with a sharpie/straight edge. works everytime.
* anticipate the issue, pause the printer when it starts to print the sets of marks, and put down tabs of scrap white media, and unpause to let printer print the marks on top of your tabs. works everytime.
* my favorite, and easiest way, is to put a piece of white vinyl/masking tape on the underside of the clear backing when the cutter doesn't recognize the trans. print. noted: this works 50/50 as sometimes it STILL won't read it for some reason.