That is the sad price paid with having adorable cotton based PUL. DWR and sprays are only said to last 20 washings. (I always dwr, then after sewing spray the leg casings in the stitch area) They can last much longer but it always depends. I have some diapers that I have had to spray after 20 or so, and some I never had a problem with. Sandi had a great idea with brushing the stuff on! I generally use nikwax since it is available. In a pinch, for my own stash, I have used the waterproof spray you can get in the walmart camping department... but I didnt use it on the leg casings since I didnt feel good about this going close to my kiddos skin.
A cheaper option is to make a potent solution of fabric softner and water and rub a *small* bit into the stitching area. air dry it and then put it in the dryer for a bit. I've only done this a few times and since I rinse with vinegar every so often there is no build up from it rinsing to the fleece. But that is *my* experience
make sure a few things though. If the inside is soaked and he is wicking through the legs then DWR isnt going to help you as much as changing more often or a heavier insert. I have those heavy wetters so I feel your *pain* LOL. I change them in the middle of the night and they are just as soaked then as when they wake up in the morning.
another problem I realized is to make sure that after putting the insert in make sure it is spread out totally. If your guy is mobile then sometimes an insert (especially if you use a trim option that is few layers) will slide and bunch in the middle and urine is hitting the stitching before it has a chance to be absorbed
HTH
Aherne