Do Multiple Hard Inquiries for Same Credit Card Application Count as One Inquiry for Credit Scoring Purposes?

This is in the United States.  I applied for a credit card but unbeknownst to me the CRA(s) had placed a fraud Alert on my report after one of them was hacked and then as "compensation" they provided one of those ridiculous Identity Protection products for free and I was dumb enough to accept. The fraud alert requires any lender to contact me by phone, but CRA did not include my phone number in the alert/personal statement, so my application was set to pending status and I needed to call in to Application Processing team, who then informed me of the alert and that I needed to contact the CRAs and have the alert modified or removed to proceed, which I did. I was also told that an additional hard inquiry would be needed to re-pull my credit report/score to proceed with application, which seems wrong, but not under my control.

 

So main question: will two or more hard inquiries from same lender for same application be treated as a single hard inquiry for purposes of calculating credit score? Or will I end up with multiple hard inquiries which would have the effect of misleadingly dragging down my credit score for a couple of years?