It's not exactly what my case is but try to analyze mine and see if this will work for your brothers case,
When I was about to get married to my now-husband (American citizen) I used the "Late registration Birth certificate" that my mother obtained when I was enrolling in college back 1998. Reason we have late registration is because the City Hall where my original birth certificate is was burnt (so they can't give me original copy and when they look at database I have no existing birth cert,)
Fast track to February 2007, since I am getting married I went to local NSO office to obtain copy of my birth certificate, and yes it shows the "authenticated late Registration" copy from 1998. It was Around middle of April 2007, I was staying in Manila and have to finally file I-130 so I decided to go to NSO Main office in Manila, to my surprise my Original birth certificate showed up in their system so there are complications between my Original and Late one-- Time of birth, Doctor's name, and Municipality where I was born because back in 1998 my mother registered me at our town not in the original city where I was born because for a late registration to go through there should be folks who knows you so practically I am unknown in that city where I was born so I have to be registered in the municipality where I lived and stay my whole life.
Well, to make the long story short, like your brother I have 2 existing birth certificate with complicating/contradicting facts but then since I used the Late registration birth certificate with all of my application with USCIS, there were no problem at all as long as it was" authenticated copy from NSO". I had been successfully petitioned and issued with Greencard now.
It means if NSO authenticate both, I guess it's NSO's fault and your brother just had to chose which he will permanently use.