I would guess and hope that your trees will be alright and will probably grow more next year. I don't think covering the graft unions is hurting anything right now, although in the long term I do think you'll want to uncover the graft unions to prevent the trees from growing too large. If the grafts are covered with soil, the wood above the grafts may take root and you'll essentially have 100% height seedlings instead of whatever rootstock you actually intended to have. What I might consider doing is moving back a lot of the soil from around the base of the tree to uncover the graft union, and then fill this up with a little gravel immediately adjacent to the trunk to allow drainage, and cover the rest (a circle of perhaps 2-3 feet radius) with wood-chip mulch. So then you'll have drainage to keep the graft union dry and prevent rooting of the scion, while providing a beneficial weed-free zone over the young roots. How does that sound?