Although the theory made sense, he wasn't convinced.
Literal
Theory [topic-は] made-sense [concessive-けれども], he [topic-は] wasn't-convinced.
理にかなっていた (made sense/was reasonable) uses 理にかなう — a set expression. けれども is the concessive conjunction. 納得しなかった (wasn't convinced) uses 納得する (to be convinced/accept).