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I have an apple tree that has had all the lateral branches eaten by deer below 5 and 1/2 feet high. I would ideally like to have branches lower for future harvesting but I don’t know if I should prune it lower (now that it is fenced in) to essentially a whip and try and have the tree start again. Any guidance would be appreciated.

I have no idea if an apple tree can be encouraged to sprout new branches lower down the trunk. Would there be any potential viable buds? Is it possible to force new bud formation by techniques like scoring the bark?

How old is your tree? Is it grafted on a dwarfing root stock?

I feel like the method I would consider first would be to pull down and train the current and future tips of lowest branches with weights and/or tie downs so they arch and allow the fruits to hang within reach. And prune in the future into open/vase shape and limit the height of the tree.

If you can post some photos, it might be possible to evaluate and make recommendations easier.

Depending on your location and weather ..

. you may need to anticipate some frost damage that would need to be cleaned off before spring growth.

This may be especially true on the already damaged branches.

Steve