In a new update, the CRM Utilities for Visual Studio now supports multiple connections per project. This is useful when you have multiple folders within each Visual Studio project, all linking to different Dynamics 365 Organisations.
Within the Web Resource linker window, you can now swap between connections and link a local solution file with a web resource from different organisations.
You can only link a file to a single organisation.
Also, in the options screen for the Class Generation tool, you can also specify which connection to connect to when generating classes.
You can download the new version below :