I had a similar problem with my cat. She lost hair in straight line from her neck down to her tail. I took her to the vet who advised me that my cat had been burned.
It turns out my ex husband was abusing her and had burned her with boiling water. I left him, by the way, and am happily divorced.
If there are others in your household, I implore you to make sure no one is abusing the cat.
edit: I hope I did not sound accusational, and I have no doubt you love your pets. I was equally boggled by my cats hair loss and felt compelled to tell you.
Your cat may have gotten a fungal infection that he's managed to fight off on his own. You mention that the fur is growing back and that's a good sign.
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