I have a website that has all URLs optimized and 301 redirected from nasty URLs to clean ones. However, everywhere throughout the site the unclean URLs are linked in menus, content, products, etc. Google currently has all clean URLs indexed, along with a few unclean URLs too.

So the site still has linked everywhere the old URLs (ideally this wouldn't be the case but this is how it is ATM).

I would like to block the unclean URLs with robots.txt.

The question: if I block these unclean URLs with the robots.txt, when the entire website is linked with them (but they all redirect to the clean version), will this affect the indexing status at all?