we have a borrower with 2 loans - we received the proper notice requesting 6% max interest rate relief on loan #1. The borrower didn't mention loan #2. I think we have to reduce the rate on loan #2 also - we have the proper notice they are now in military - they just didn't mention the 2nd loan.
What do you think?

I say yes. The bank has knowledge that the borrower is covered under SCRA (proof of orders or whatever your bank requires) therefore the borrower has done what they should & the bank then must comply with SCRA. Not applying their rights because of an oversight on their part - very bad PR.

Yes you do need to reduce Loan #2's rate.

I don't think you are obligated to if the request you received was specific as to loan no. 1. That said, remember the SM could come back later and ask for that protection retroactively. Personally, I'd send them a cordial letter thanking them for the request, their service and I would denote that you have applied these protections against BOTH loans. If for some reason they don't want the second loan included, they should notify you.

I assume both loans are such that they are covered and one wasn't entered into after entering the service. It could also be that someone else is making the payments on that loan and the SM didn't feel protections were needed. (Example - John joins the military. Gives his car to his brother to use and pay for while he is gone. He didn't think 6% was needed. Who knows?)