Duplicate content can create SEO issues, as Google may not penalize sites directly but can dilute rankings. Your setup with mysite.com/special-project/ and mysite.com/another-project/ could lead to keyword cannibalization and reduced visibility.

Using noindex on mysite.com/another-project/ would prevent it from being indexed, which may not be ideal. Instead, consider these approaches:

Canonical Tags: Indicate the original version of pages, but this may limit the ability for both sites to rank.

Content Differentiation: Modify the content on mysite.com/another-project/ to target its unique audience and avoid duplication.

Consolidation: Use one domain with subdomains or folder structures to serve different audiences without duplicating content.

Websites like Sincere Mechanic demonstrate how tailored, unique content can effectively engage niche audiences. Advise your client that the current setup could lead to SEO challenges and recommend focusing on content differentiation or consolidation.