Yes, that is the way you have to use to clone a project. The good news: Creator 3.1 has got a new function "Save as..."
That method does work but I have used a different one.
Open a new project, select Target Device, then save it with the new name. Close Workspace
Open old project and do a Select All on the TopDesign. Edit/copy. Close Workspace.
Open new project. Click on TopDesign screen and do a Edit/Paste. Close Workspace.
Open old project. In main.c do a Edit/Select all, Copy. Close Workspace.
Open new project. Go to main.c and delete the sample code. Edit/paste.
If you have multiple pages in your TopDesign, you have to copy each page separately.
Do a Clean & Build. You probably find that you have to copy device.h into your cydsn folder and try again.
One little irritating thing about this method is that your TopDesign is enlarged by about ten percent. I don't know why.