I am having this issue with my sample quilt. The first 3 blocks I used the frixion pens to mark the stencil pattern, since the blocks were busy, I had a difficult time trying to see the lines - did not like it. So I switched to my Pounce in white. I am using plastic stencils, so I wiped a smear of white pounce chalk over the stencils, it made clear thick lines which made it so easy on my eyes and hand quilting was a dream.
I tested the frixion pens by washing a test block, dried it, and then put it in the freezer. The marks didn't appear. I did the same with pounce, and it washed off easily. Would need to know what type of transfer are you doing? If you are doing quilting by machine, I would mark my design on tissue paper (or tracing paper). pin it to the quilt and sew right over it.