Poor kid. That's a lot of wing to be missing. While I don't have experience with that sort of birth defect, I do have experience with flying difficulties due to morbid obesity and resultant muscle atrophy, injury, and weakness due to neurological issues and bad flight feathers.
From my experience, with enough time and exercise, they can regain some, if not all, of their flying ability. Trimming her good wing to even things out sounds reasonable. Even though she has a birth defect, I definitely wouldn't clip her wings, except to make her good wing semetrical with the bad wing. However, you have to keep in mind that if you do let the good wing's feathers grow out after clipping them, they'll be prone to injury and breakage since any new flight feathers coming in won't have the protection of surrounding fully grown feathers.
I'd definitely make sure he exercises his wings at least a few times a day to build up muscle (maybe do it on some newspapers on the floor so he doesn't hurt himself). Hopefully, he'll eventually be able to fly. Although he'll never be able to fly as gracefully as a budgie, hopefully he'll be able to do short flutters from perch to perch, and be able to gently flutter to the floor if he ever falls.
When poor Rumi had her neurological episode, she became very weak and completely lost her ability to fly, and it's had a huge impact on her life. She became very insecure, and she became incredibly aware of how much her life had changed. Luckily, she's slowly grown stronger (she has her balance back, her feet and legs are strong again, and she can bite unbelievably hard again), and she's learned how to use her wings to push herself up while climbing, and she can now fly short distances (around a foot or so). From my own experience, a bird who can't fly (excluding flightless species) doesn't have the best quality of life. I'm not saying to euthanize those who have lost their ability to fly, as they still have a great life (heck, blind, legless parrots can still enjoy life!). I'm just saying you should definitely try to help him be able to at least fly from perch to perch.
Heck if morbidly obese Lara (I honestly thought she could die any moment from heart disease) could lose all that weight (you have no clue how grossly overweight she was. She would get out of breath just walking across a perch. She actually jiggled when she moved, she was so fat), and regain strength in her atrophied wings, I'm sure your boy could eventually fly short distances. Anyways, good luck with the little guy!
