Database Connection String crossing Targets

I have defined a database connection to my local instance of SQL Server and a target to an Azure instance, in the same project. When I publish to the remote target, I get an error connecting to the database and when I ftp into the site and inspect the files, I see the connection string is from my local target.
The connection file I’m looking at is:
App_Data\ServerConnect\modules\Connections\dbNorthwind.json

Pull the file down using FileZilla and enter the correct credentials and upload it again, and it works fine.

This is in 4.0.1 on Windows PC.