I would not use a Clorox pen on the fabric if it is a bleach pen. The bleach will weaken the fibers where it is applied. The fabric will appear fine for awhile, but eventually holes will develop in those areas.
Embroidery floss is similar to fabric in that the dyes may not all be set. Excess dye -- beyond what could be chemically set into the material -- is what you see when it bleeds or "crocks". Crocking is where dye rubs off onto something else even when there is no water present. Basically the manufacturers super-saturate the floss with dye, then subject it to chemicals and/or heat to "set" the dye. If they don't rinse the floss or fabric afterwards, whatever dye the chemicals didn't set will be excess.
Your mother's quilts may have done the same thing but, because they were washed in quite a bit of water the first few times, the bleed would have been so diluted by the wash water it would not be noticeable and the excess dye would have gone down the drain with the wash water. The reason you are having this problem is because the floss got wet and then was in direct contact with fabric. There wasn't enough water to dilute it, and the dye settled in the fabric rather than going down the drain with wash water.
I think you have a good chance of getting rid of the bleed by washing in Synthrapol when the quilt is finished. Most dyes these days are set by chemicals and/or heat. I woud just be careful to keep the unfinished quilt out of direct sunlight; you don't want it heating up before you have a chance to wash it.