"Checking up on someone", usually indicates that you want to see if that person is doing what he is supposed to be doing. g. I'm going to check up on my son and see if he's finished his homework yet.
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"Checking in on someone", means that you want to see if someone is okay. e.g. I'll check in on Mr. Jones today and see if he has enough food for the week.I am assuming I can use the term 'checking in on' even if I want to know if a person is financially okay.
Probably we need a bit more contextOne of my friends lost his job a month back. Somebody was inquiring about him.