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this is usually a problem with the large fan, because the large fan has the fan control module built into it, do you have a scan tool to check for faults?
that is what I am saying the large fan is the thing that turns on the small fan so if the small fan is running then the problem is in the large fan, the large fan is the relay for it,
The scan tool at the auto parts store sometimes do not read all the codes that are stored you can try it, I would replace both of them