Reproduction steps:

1. Open the attached project (it has an empy script in the "Resources" folder)
2. Build to a folder
3. Try to run from VS
4. Fails with the following output:

1> Copying unprocessed assemblies...
1>D:\_BUILD\New Unity Project 1\New Unity Project 1.csproj(245,5): error MSB3030: Could not copy the file "D:\Projects\New Unity Project 1\UWP\Assembly-CSharp\bin\x86\Release\Unprocessed\Assembly-CSharp.dll" because it was not found.
========== Build: 0 succeeded, 1 failed, 0 up-to-date, 0 skipped ==========
========== Deploy: 0 succeeded, 0 failed, 0 skipped ==========