Every time I have to link a file into an ASP.NET project as link, there is always something I forget to do, because Visual Studio is way too buggy and annoying with these. T
If the goal is to include content folders (e.g. scripts, images), then you should not manage the individual files. Instead, include these folders in your build and publish files.
When files need to be added/removed, simply update them in the content folder. This is essentially how we handle Help files since they are not managed by the developers.
Check out these links:
Is there a way to automatically include content files into asp.net project file?
ASP.NET Web Deployment using Visual Studio: Deploying Extra Files