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You will have multiple inquiries on your report, but yes it will only count as one for scoring purposes. Depending on which FICO scoring system lenders are using, you have either 14 day span, 30 day, or 45 day span to rate shop. So it play it safe, make sure you do all your applying within 2 weeks or all in one day as you plan to do.
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Nice job paying the loan down.