My understanding agrees with @parentologist. I think that you will need to send two high school transcripts (one from each school), and university admissions will look at your son’s actual grades along with the profiles from both schools.
Different high schools in the US compute GPA in wildly different ways. One daughter attended a public high school where a 97 in a regular class is an A+, but only counts as a 3.7 towards the GPA. This did not seem to matter at all when she applied to universities. At one point talking to a colleague I was surprised to discover that his daughter had a 4.0, but then found out that at her school a 90 is an A-, but still counts as a 4.0.