Old question, but I had the same problem just recently.
There must have been an issue in your Assembly-CSharp.csproj or project-name.sln files. Most likely to be the .csproj file. If you take a look at it, you will see various references to .dll files.
You can tell Unity (my version: v2019.2.20f1) to create these for you by enabling Edit > Preferences > Generate all .csproj files.
1. Delete both files.
2. Enable .csproj file generation.
3. Double click on a script in Unity.
This fixed my issue.
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