My goal is to figure out the best way to add protected content using a subdomain. I have an established website (mydomain.com) that has article abstracts and author info for seo purposes. I'd like to add a button that redirects to a new subdomain (journals.mydomain.com) that contains PDFs and is completely password protected (so noindex). Is this best practice or will my main website be penalized for redirecting to a protected subdomain? Is there a better approach?
By doing that you'll just be linking unreachable content, in fact that the same workflow than the private sale website so don't worry. If you want to gain the max you can try the same process than the news paper : give the document to google but not to user if it's possible. Else, just try to link only to the connection page google will naturally understand the lock