I have a year old apple tree, that I have been growing in a pot indoors from the seed. I noticed that it was completely stunted compared to her other two siblings a week ago, so I took her out of her pot and found that the soil had clay in it and it was restricting root growth as the clay was just clamped on to the roots (roots were yellow with a couple of white ones). I took her out of the pot, ran some water on her roots to wash all the clay away and freed her roots. Then I replanted her in fresh potting soil. That was four days ago, the leaves have wilted and they are now turning yellow. I expected some stress shock, as it was really difficult to get the clay off of the roots and realistically, even though I was really really careful, the roots probably have damage. That being said, it's breaking my heart not doing anything about it, she looks like she's dying, and I'm wondering did I over-water her when I replanted her? could that be the reason? I read that some folks are saying to cut the main stem in half, to stimulate root growth, but I just don't have the heart to do it. I would really appreciate any help.

Maybe Robert can help with this question?
@robertduval14'

I'm sure you damaged the roots. The only thing you can do is to continue to care for it and hope for the best.

Sounds like severe transplant shock. Apple trees generally don't respond too well to it on this level. All you can do at this point is care for it as you normally would and hope for the best.

Give this article a look over...
http://www.goodfruit.com/preve...

Maybe keep it in the shade and cool until it perks up, which we only can hope for.

Don't fuss over it, and absolutely do not give it fertilizer or anything but a little water as needed. A stressed plant can't use fertilizer and it will burn the leaves.