1. Is is possible that part of the problem is parasites/bacterias and that's why changing programs works temporarily. Different freqs may be working on different items or in the case of parasites, the different stages of the parasite.
Your statement that day is generally not a problem but night time is, leads me to think that the subconscious needs some prompting. Try having a calendar that the boy uses to color or somehow mark the days for 'dry' nights and 'wet' nights. You should know within 30 days if this helps.
2. From your description it would appear that for some reason while asleep he isn't getting the signal to wake up and go to the toilet. Another possible reason might be is the muscles in the bladder are relaxing at night whilst sleeping. As he doesn't have this problem during the day whilst awake the problem is most likely in the brain. What programs have you tried for the brain?
As to why the programs you have tried result in a temporary fix is another puzzle. Has he tried hypnotherapy?
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