I had an android project in this address:

*D:\AppsFolder\MyApp*

Then I copied the containing folder (via Windows file explorer) to this address on my Desktop:

*C:\Users\User\Desktop\AppsFolder\MyApp*

When I made some changes to Java classes of the copied project, the changes were also applied to the original project. 
I noticed that in the Android Studio's title bar, the address is a mixed of both:

*MyApp [C:\Users\ ...\MyApp] - D:\AppsFolder\MyApp\app\src\main\java\ ...\MyClass.java [app]*

What is the problem? How can I create a fresh new duplicate which does not affect the original project? And now how can I revert the changes of the original files?