Question

How can we get two exact copies of the same project uploaded on the server with different GUIDs ?

Answer

It is correct that you cannot upload another copy of a project to a server that already has that project. The project has a GUID, and the server will not allow two projects to have the same GUID value. So while we might be able to upgrade a local copy of the project, we would not be able to put it back on the server.

However, this can be bypassed while using FC Admin Tools UploadProject call, 
More info on that:UploadProject

Specifically, there is a /CheckProjectExists flag which is disabled by default, and if we will be uploading a project to the server where the project already exists without this flag in the command then the existence won't be checked. If the GUID will match, then for the newly uploaded project a new GUID will be created, therefore we will have two similar projects on the same server with different GUIDs.

Note: Make sure to change the name of one of them just to avoid further confusion.