Why does unity delete additional files after running a standalone build

I need to deploy some additional files beside of a standalone unity executable. If I build the executable manually using File\Build Settings\ and Build, the files are found at runtime with no problems.

When I attempted to automate this using BuildPipeline.BuildPlayer(scenes, path, BuildTarget.StandaloneWindows, BuildOptions.None), the executable should be created just as if I had done this manually. I later copy over some of the extra files I need into the Assets folder.

However, upon running the executable, the extra files that I copied over are deleted from disk. This does not happen if I build manually from the UI. Are there different BuildPlayer build options that I should run to create a standalone windows executable?