What happened:
Missing prefabs when you open a project from scene file

Steps to Repo:
1. Create a new project with two/three prefabs. Save the scene afterward.
2. Create one more new project with similar prefabs. Save the scene.
3. Now, from the explorer go to the first project and double-click the scene file.
4. A dialogue box will open up. Click Open.
5. Now after opening the project no. one goto
File > Open Project
Open the second project again and observe the previous scene with missing prefabs

Expected result:
Opens the scene of currently opened project.

Actual result :
Opens the scene of a previously opened project.

Versions reproduced with :
2018.1.0a3,
2017.3.0b8,
2017.3.0b7,
2017.3.0b6,
2017.3.0b5,
2017.3.0b4,
2017.2.0f3,
2017.1.0f3,
5.4.6f2

Environment : Windows 10