I also report this issu to the Visual Studio's Developer Community, but didn't recieved a response yet.

The relative path to the "System.Data.SQLite.Core.targets" is set automatically in the csproj when adding your nuget to the project. I didn't changed anything.

I also tried to build without "parallel build" it didn't change anything.

Did you reproduce the bug with the minimal project I sent you?

Here is the "step by step" bug I sent to VS2017 :

- Create a new solution (Windows Forms .Net 4.6.2)
- Add System.Data.SQLite version 1.0.108 or higher (it didn't work with 1.0.109 neither)
- Build project : the x86/x64 folders are in bin/debug (it works in this case)
- Close Visual Studio
- Remove folders
- Open solution / Restore nuget / Build : The x86/x64 folders are missing.

The behavior after a clean in Visual Studio is not always the same, sometimes after cleaning the solution and building again make them appear, sometimes not.