It is normal for a rabbit to expeirence a major shed twice a year, known commonly as a "coat blow." These major sheds occur in response to the bunny's circadian rhythms which are priomaril influenced by photocycles, the amount of sunlight vs dark in a 24 hour day. Coat blows commonly occur in Spring as you bunny has normally done before, and again in the fall. Therefore, what he is experiencing is just likely what he is supposed to do this time of year in perparation for the coming short photocycle - lose his summe rhair and grow in more dense winter hair.
Why he did not experience a normal shed in fall before I cannot say for certain, , but circadian rhythms and natural occurrences can be thrown off by circumstances such as the presence of artificial light, or stress induced by noise or unusual circumstances that are new and novel to the bunny. Genetics can also play a role in circadian rhythms, where ibred pines may not necessarily exhibit normal rhythms and hence may not shed when we expect them to.
I do not think that the shed is the result of the urine in the box, as hair loss from "urine burn" typically causes redness of the skin and hairloss at the hind quarters focally, not general shedding.
What I would liek you to do from this point forward is monitor your rabbit for signs that the shedding may be beyond normal seasonal coat blow. Any presence of focal areas of complete baldness, redness of the skin, sores on the skin, flaky skin, or crysty appearance of the skin.
Any of these types of lesions could indicate infection with mange or other mites, bacteria linfection, or ringworm. If such lesions apepar at any time, you should therefore have the little guy to the vet for examination and skin scraping.
Veterinarian
Licensed Veterinarian, Practice Owner, And Book Author ("Canine and Feline 101")