To reproduce:
1. Create new project
2. Create new C# script
3. Right-click script and choose "Open C# Project"
4. Right click "Solution 'New Unity Project'" (the root of all) -> Add -> New Solution Folder
5. Create new project in newly created folder (simplest example would be a console app)
6. Close Visual Studio, a popup asks if you want to save changes in the solution. Click yes.
7. Close Unity
8. Reopen the same project
9. Double click NewBehaviourScript.cs in Unity to open Visual Studio

Expected: The structure should have been unchanged
Actual: New Folder created in step 4 is missing and project created in step 5 is pulled out into root

Reproduced in 5.5.2f1, 2017.1.1f1, 2017.3.0a7
Tested on VS2017 - https://i.imgur.com/tVK8Z8O.png