I have used frixion pens a lot. In fact I used them on my most recent quilt which I posted photos of on the CW topic here on TQS. I used the friction pen in the white, yellow and purple areas. I use a steam iron to remove the markings when I have finished quilting. I have sent several mini-quilts from Ireland to America and none of them (as far as I know) have had the markings return. I even checked with AAQI when I sent one and then read a topic about it here, but the quilt was fine according to them. So here's my view, I make quilts to be used, not for exhibition, most of the time. When I use a frixion pen on a utility quilt which I give to somebody as a gift I tell them that if marks ever appear they should iron the area with a steam iron or wash it, whichever they prefer. As for the long-term effect, I won't be around to witness it. Who knows perhaps the thread or fabric will disintegrate before the frixion pen lines do the feared damage. I always recommend that my quilts are washed in the washing machine at 30ºC and dried in the tumble dryer until almost dry, leaving the last bit of drying to be done in the air. This is what I do and I have never had a problem. But I always prewash my fabrics (not my batting).
I wonder how much testing has been done on the blue water-soluble pens that all the professionals use? Or the blue air-soluble pens?
As for marking a dark area of a quilt, I use the Bohin chalk pen. I have found this the best because it comes off easily with a wipe with my Machingers gloves. If that isn't enough then I dampen a microfibre cloth slightly and use that. I don't know how chalk works with silk BJ so I can't help you there. I have used the Sewline white, pink and yellow fine chalk pens and found that the yellow and pink don't come out, particularly on white fabric. So now I stick to the Bohin chalk pen. If I am going to think about entering a quilt in a show I will use either the blue water-soluble pen or a mechanical pencil.
Just my tuppence worth.