Similar situation here.

DH and i fell is love with Charlie for our DS2's name but the only thing was we have a niece called Charlize and she would often get Charlie. She is a niece that we actually see quite regularly also.

We angonised over it for a little bit but nothing ever changed the fact that we loved the name and at the end of the day it was our choice.

So when DS2 arrived he was named Charlie and we did explain that we definately thought of the resemblance to our niece but loved the name so much. It was fine with all the family as far as i am aware.

If anything now most (even myself) refrain from actually shortening her name so much now. I think her parents still may call her Charlie at times but she also gets Cha Cha.

In your situation it sounds that there is even less contact with your brother. Go with it if it's what you want

And now that i think of it my SIL's stepsister also called her little boy Charlie, so they may or may not have been thinking the same thing when choosing his name.