Look in the RuntimeLog. You should see an exception near the top while the project is loading. Look at the exception - it should give you clues as to the problem. Often, you can make a small change to an automation and re-save it to clear deserialization exceptions.
I am not sure what causes this but it is relatively rare. A simple way to fix this is to add the missing dll as a miscellaneous file to your project. This will cause it to be distributed with the deployment package. On the project properties page, click in Miscellaneous files and add the file - you can find the correct location by looking at the path for the reference.
The dll is not located in the Pega Robotics installed folder. So, to add the dll under Miscellaneous files from : after copying dll in the installed folder or from C:\Windows\Microsoft.NET\Framework64\v4.0.30319 (for this dll only).