I had thought he wouldn’t come to the meeting.

had thought有一种“我本以为”的含义。否定词宜否定从句，不宜转移至主句。

I often think you are not fit for that job.

I do think you shouldn’t do that.

总结起来就是，当句子为疑问句或think以thought, was/were thinking出现在句中，或有副词强调助动词do修饰时，think不能否定转移。

I do think he isn’t a doctor. 我确实认为他不是医生。

I really think you can’t answer the question. 我真以为你不能回答那个问题。