Because the converter removes the Christian/Islamic Syncretism doctrines from faiths if the respective religions don't exist in Imperator, this can lead to faiths like the Basque pagan religion only having two doctrines.
Possible fixes might be having the Syncretism doctrines removed by created a new faith definition in the converter_faiths.txt file that overwrites that doctrine with something else, or maybe having a game start on_action that adds in a replacement doctrine if the syncretism doctrine isn't there at game start.