Hi Mkyol, You're telling about an incident that happened in the past but that doesn't prevent your using more current information to describe the professor. I think "has been helpful" is the better choice, stressing the ongoing relationship. If you say "had been helpful" it seems to suggest that you weren't really sure whether or not he could still be of help.
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Mkyol"So I considered carefully what to specialize in at the graduate school, and I met with a professor who had been/(has been) a lot of help to me and sought his advice."
I was kind of under the notion that if I use 'has been' in that sentence, it doesn't really agree with the past form of the sentence, so it's somewhat of a bad or maybe unnatural form.