So i recently converted a Ck2 Game and my vajrayana tibetan empire became a thevara empire Eu4 as well as other vajrayana nations. Anyone has a fix for this issue?
No.
Exporter cannot recognise between branch of buddhism.
Its impossible to mod, you'd need to script your own converter from scratch.
Only alternative is editing exporter-created EU4 mod. By yourself. By hand.