One thing to remember when publishing your ASP.Net web applications, you may find out, some files could be not completely published due to the settings on the file properties. One example that I had are some font types file. In order to fix this problem you can navigate to the files that are missing and right click the properties.

As shown in below image, in the build action mode, please select the option content rather than None. By default None option is selected.

Once the option has been selected, you can re-publish the project and the files should be up there.