It should be fine. Cut them back to small shoots if you can as this will allow the shoot to provide some apical dominance and reduce the excess response of vegetative regrowth at point of cuts. Come back in July and cut back any vigorous surge of water sprouts or just rub them off as they appear during the growing season. That is the sprouts that appear near the cuts, hell bent to return the tree to its previous height.

In the spring of 2012, I attempted to graft a Pear scion onto my apple tree using Winter Banana Apple as an inter stem. (All of he grafting i do is "Whip and Tongue" grafts wrapped in grafting tape. I then coat the wrapped union with grafting wax) The parent branch was a Winesap Apple branch with a grafted Winter Banana Apple scion from a few years before. (I actually have two of these paired branches.) I then attempted to graft two "Kieffer" Pear scions onto my two Winter Banana Apple inter stems. The "Kieffer" Pear scions started to grow, but died a few weeks later. This spring (2014) I attempted to graft this Apple / Pear union again using the same Winter Banana Apple inter stems. I had just enough branch on my Winter Banana branches to try this experiment one more time. This time around, I used "Sunrise Pear" scionwood. The grafting was a screaming success! (I had enough "Sunrise Pear" scionwood to graft two branches onto my apple tree, and two more onto an ornamental pear. All four pear grafts were a success!) I have no idea why this experiment failed in 2012 and was a success in 2014. I do not know if it had to do with the pear variety used, or if it had to do with environmental circumstances. I will re-post in 2015 with an update. There are a few different treads on this subject so I will be re-posting on those threats also. Below are pictures taken on 07/27/2014.

So in the training of the water sprouts, do I treat it like a large bonzai, and weight or tie down the sprouts as the grow? Any branches that don't now bud and start growing, shall I remove them as summer progresses, or just leave them till next fall? My soil is Georiga Red clay, a compaction problem would be an understatement, as to uncompacting it I don't see how it could be done with an established tree, if It was ruined by me, and doesn't turn around in a couple years, I'll remove it and plant some more in better locations, at that point, I'll assume I could fix the compaction problem via tilling a large area prior to planting?

Hi Ed- I will lend some experience to my 4-1 apple. Last year my 4-1 looked like this on the main scaffold of all the 4 types. It was almost like the tree was damaged somehow but the ends were just like your tree and leafed out properly. I had probably a foot of just branch with no leafing. I waited until late November and cut them back quite substantially and it leafed out properly, flowered and now has apples. So, I would probably just let it go until dormant, then cut. It worked for me. With a tree that young its really about the root development and removing 30% of the leaves can't help early summer.