Steps to reproduce:

1. Open project.
2. Open Scene "Mini" in folder "_Scenes".
3. Press File -> Save Scene as..
4. In navigation bar type "...\Assets\_Scenes\Mini.unity" and press enter. <---- IMPORTANT. After typing and pressing enter, check if it ends with "\Mini.unity"
5. Set file name to "MyScene". (File name does not matter)
6. Press Save.

Expected result: Scene will be saved in folder "_Scenes".
Actual result: Unity crashes.

Reproduced on 5.3.0f4, 5.3.6f1, 5.3.7p1, 5.4.3p3, 5.5.1p1, 5.6.0b6.
Regression found in 5.3.
Works fine in 5.2.5f1.

Note:
It was reproduced on Windows 10.
Make sure that .unity files are opened by Unity.