Same problem here. Most of my birds had some degree of yellow in their soles as chicks, and have lost the yellow as they aged.
I am grateful for wing tags. This is my first year with chicks from my own breeding pairs. I have been wing-tagging them when they are a few days old, and making notes about skin color and sole color. That history has been valuable. A dog killed all of my promising potential breeders this year. I am left with mediocrity. Despite the white-looking soles of the remaining birds, I know most of them showed some yellow in their soles when they were chicks. So I know there is some yellow in their genetic makeup and I can probably use a couple of them in a breeding program without losing that trait entirely.
I did notice that the young chicks with yellow in their soles also had yellowish combs, and the young chicks with pink soles (no yellow) had pink combs. That seemed to hold for the first week or two, until the faster-developing chicks started to grow out their combs and wattles. It is my understanding, possibly wrong, that the yellow skin gene is the same gene driving the yellow in the sole. Not sure if I am blowing smoke or not, but it seems to make sense that a young, yellow-skinned chick would have a yellow-tinted comb. I'm wondering if comb color in 1-5 day old chicks would be a reliable way of telling if a bird has that yellow-sole gene, even if the yellow in the soles is really faint? In my young chicks it was easier to tell comb color than foot color. I will have to pay more attention to this in the future, to see if there is a correlation. Has anyone else tried to use comb color in 1-5 day old black java chicks to make decisions about sole color and possible culling? Does this make any sense at all?
I have been using marigold petals sprinkled on their feed for a few months. Haven't noticed a difference. Probably not using enough to have an effect. Will probably stop when I run out of petals. A pound of marigold petals is expensive, even if it does go a long way.
Now that is interesting. I had not paid much attention to the pink comb/yellow comb thing. But I hatch more Mottleds than Blacks and I don't have as many problems with pink feet in the Mottleds as I do the Blacks either. But our Mottleds with darker coloring, especially my project birds, have more pink feet issues than the rest of the Mottleds seem to have.
I've got a dozen Black chicks that I hatched about a week and half ago and I was looking at them and thinking that I should band a few of them now so I could watch them as they grow. There are a few that have a lot more black on them than the others, and I'm thinking that either those are going to turn out to have dark eyes and be closer to what a Black should be, or they are going to be carrying the other genes that caused non-standard feather coloring to show up.
So now I'm gonna have to watch and see about this color of comb thing and see how that works out. Another thing to do.

Yes, I looked at getting marigold petals and they are not cheap. Between having multiple bloodlines and multiple colors, we've got a ton of birds and it would cost me a fortune to buy marigold petals for all of them. The hubby told me to just grow my own which I may start doing since we already garden.
Did you end up with enough birds left to be able to hatch in the spring?