[4doggiemama]

I was able to find a little information. Just googled dog penis amputation. There actually is a reason for it and it sounds as if what your doggie is going through is one reason. Also sounds like it is hereditary. If I'm right the clinical name for your doggie's problem is Paraphimosis.

Canine Penis And Prepuce - WSAVA 2004 Congress

Small animal paediatric medicine and ... - Google Books

AVMA - Journal of the American Veterinary Medical Association - 230(3):375 - Abstract a quote:
Treatment and Outcome—A midline preputiotomy incision was used to expose the penile shaft; amputation was performed caudal to the preputial fornix. The terminal portion of the urethra was anastomosed to the preputial mucosa, which allowed the dog to urinate through the preputial orifice.

Clinical Relevance—Unlike the more conventional urethrostomy procedures performed in dogs, preputial urethrostomy eliminates the potential for local skin irritation during urination. Preputial urethrostomy is also easier to perform in those dogs in which penile amputation is required adjacent to the preputial fornix. A release incision cranial to the prepuce can be used to facilitate caudal displacement of the preputial mucosa, which facilitates urethral anastomosis to this structure. A midline preputiotomy incision provided excellent exposure of the penile shaft for this surgical procedure

Well, I actually learned something. I am so sorry that your baby has this problem. Kisses to him. ~Joanne~