It would appear that you used one of the disappearing markers .... after so many minutes it vanishes!
The info about that would have been on the package when you bought it. I'm sure it was heart breaking for you ... a lot of work to do all that marking!
If you're wanting to use the frixion pens ... try it on fabric samples of the quilt you are attaching your yo-yos to and see if you are happy with it. Duplicate whatever you have done to the fabric ... ie. washed, dried, starched, etc. Then mark with the frixion and iron it away. Also, launder to see the after effects. And a trip to the freezer might be worthwhile too. Then make your decision.
The markers are great ... and give such a nice thin precise line.
If you're attaching the yo-yos to the side where the markings are, then all will be covered up. If so, then why not just use pencil?