Apparently, that call is rather destructive to any additional info added to the blueprint by other mods that's not entities (like tye program for fcpu). Can you minimize your use of that call, to only run if the blueprint ACTUALLY contains burner entities to be replaced?

Can you point me to an article explaining why set_blueprint_entities is broken and the recommended workarounds?

There was a conversation about it in the factorio modding discord in the last few days, I think. I don't know if there's another way to change the entities in the blueprint, unless it's possible to apply an upgrade planner on it.