You're never gonna be able to get it to look like the seam was never there. So important to have realistic expectations. Now depends on how thick the flashing was but I have had good luck with using acetone to dissolve very thin flashing. Like thinner than a sheet of paper. Your mileage may vary. Urethane is kind of unforgiving when it comes to working with it post cure.
If you are going for screen accuracy then I would leave them on. The screen used suit had those seem lines on it all the way down to the legs. If you don't want them then I would do what Kev said above.
mineral spirits, dremel tool, fingernail scissors and a steady hand. All things that were covered already but thought i would add just because its been awhile. Hope it turns out, been where you are many times.