UC app: trimester system for 2 years of HS

Thinking ahead to September… My son attended a boarding school in New England for his first 2 years of high school. He transferred home to a California public school for his current junior year, and will graduate from here. The boarding school used a trimester system, which was a mess when the GC was trying to transfer his grades into the semester system here. She actually just doubled his final/year grades - which seems inaccurate to me. We would like to submit both transcripts with UC app in the fall, but understand that it’s self reporting. Has anyone ever dealt with a situation like this? I have multiple concerns. Any thoughts would be appreciated.