Heat from pressing only fades the marks away. The ink is still there. If the quilt ever gets cold, the dark marks reappear. You can test this out by pressing the marks and then putting the piece in the freezer for a while. When you take it out, the marks will be there again.
People have been shocked to find that the quilts they send to shows arrive with the black marks visible on them again. Probably because the package got cold in shipment.
Use your Frixion pens carefully and with this knowledge.