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Is there a way to streamline the process of encrypting the connectionstrings after you deploy a web application?

Here's the backstory. We manage many .NET websites. We move them to a development server and then eventually up to the production server. But after each site is created on the development box or the server box, I have to go onto the server and encrypt the sensitive data (usernames / passwords / connectionStrings).

This becomes tedious when you start talking hundreds of websites. Is there a better way than doing it by hand? Something that a developer who doesn't have access to Remote into the server could run after they deploy the application?

Or is this just wishful thinking?