Because I'm using the latin v for the αυ, ευ = aV / aF. So I felt like keeping the greek ν alongside the "new" v would make them hard to distinguish.

But you're right, this adds confusion. Especially for a native Greek speaker, and I'm not very satisfied with this solution.

Any suggestions?

PS. Updated site with some more info about the conversions.

Why not αβ, εφ;

Hmm yeah, didn't consider that!