Well I don't have kids but my levels have changed. Before I was eating normally, and several years later, now, I should only be eating 10 grams of protein.
When i ate normally my levels were in the teens and I was in middle school and high school at the time. Between then and now (20 years) I have become less tolerant of protein. My levels get as high as 1965 micro-moles per liter which is around 33 mg/dl. At 10-15 grams my levels are ~800 which was where my levels were when I was much younger.
So yes the do change and I don't know how many doctors believe this but it happens.
My son has classic PKU, so his tolerance is much different than what your son can have. However, my dietician has told me that we can expect his tolerance to change a bit at different times in his life. Specifically during ages when he is going through growth spurts or if he gets very involved with a sport of excercies is phe tolerance may increase. When his growth spurt stops or if he was very involved in a sport and then stopped, his phe tolerance would decrease as a result.
Both growth spurts and a change in activity level can cause phe tolerance to change. Not getting enough calories can also increase phe levels by making the body catabolic, but since you said he is getting approximately 2000 calories a day that probably isn't the issue.
Does he go to school/daycare or is he under the care of any adults other than you during the day? If so I would speak to his other caregivers to see if maybe some sort of mistake is being made on their part (i.e. not measuring his food properly, accidently giving him food he shouldn't have, and so on). Because teachers, lunch staff, etc do not live with PKU on a daily basis and have not had many years to learn about PKU like we have it can be very easy for them to make mistakes without even realizing it. When I started school my mom said that my levels increased for a while, and she later found out it was because the lunch staff was not measuring my foods properly.