Ok I will take the paper towel out and put a dry one in.
Would it help to dry the seeds first, or would that kill them?
No, it wouldn't help and it wouldn't kill them. Apple seeds need cold stratification and that is exactly what you gave them. If you store seeds in the fridge with the right amount of moisture, they cold stratify and germinate. Nothing will make them stop or go backwards. It is a balancing act. If you store them with low moisture in the fridge you can put them into suspended animation of sorts. They won't cold stratify if the moisture content is too low and they won't germinate well. So, if you want seeds to germinate in the spring, you need to start by storing them with low moisture content and then 60 days or so before you want them to germinate, you need to add the right amount of moisture. Too much moisture and the seeds will get mold. Too little and cold stratification will slow or stop. Some seeds/nuts that are high in carbs like chestnuts are more susceptible to mold.
Your next problem. Just before a seed produces a root radicle, it decides up verses down based on gravity. When you check seeds and change the orientation, it takes a bit of time, but the seed will reorient up and down. The root will then change directions. You can get a tap root that has major kinks in it. That won't matter when the tree is young, but these sharp kinks can constrict the tap root as the tree ages. It is similar to the problems you get with j-hooking and circling when growing trees in non-root pruning pots.
One option at this point would be to start the trees indoor under lights in a root pruning container system. Unless you are planning to do this as a winter project for a number of years, the setup cost is probably not worth it, especially for apple seeds.
The option I would consider is vernalizing them. Take a relatively deep container and fill it with medium (promix or something similar). One of those long window seal flower pots would work. Plant your seeds an inch or so apart. Then place the container some place dark and cool like a fridge but make sure it does not freeze. The seeds will germinate and produce root radicles. The radicles will grow down but no top growth will start because it is dark and cold (winter). The tender roots won't freeze because you keep it above freezing. Over the winter, the root radicles will grow slightly. You can't do this with chestnuts because the nut has so much energy the tap root will grow too deep and hit the bottom of the container. You should not have this issue with apples. Next spring you can remove the seeds from the medium and plant them where you want them with the appropriate protection and such.
Thanks,
Jack