I used various colors of Frixion pens to mark a quilt my daughter pieced from Kona solids as a graduation gift for her sister-in-law. I had used the Frixion pens on other quilt projects and the marks came out like a dream, so I never gave a second thought about using them on this project. Because of that, however, I was already half way through marking the quilt before I thought to check whether the marks could be removed by ironing. I was absolutely sick to see that the marks were not coming out! I tried water and lots of other tips. I finally just switched to another marking system and hoped for the best. I always wash my quilts afterward in cold water and then warm water, anyway. After the first wash, the marks were all gone.
I'm not sure that I would worry about the marks only coming back when the quilt is exposed to cold. My quilts are used, not displayed and preserved, and, as far as I'm concerned, a problem that can be fixed by washing in warm water is not a real problem.
Those who worry about this problem are perhaps more "archival" quilters than I am. To avoid the type of heart attack I almost experienced, however, I would recommend testing the pens to be used on the fabric ahead of time.
BethMI