If you want to save changes to the existing project, use option 1.
If you prefer not to overwrite the current project and want to save it as a new file instead, use option 2.
Option 1.
In Menu bar click File and then Save project or
in Ribbon bar press Save project or just press Ctrl+S shortcut
Option 2.
In Menu bar click File and then Save project as or just press Shift+Ctrl+S shortcut
or in Ribbon bar press on the arrow on the right bottom corner of the button Save project or just press Shift+Ctrl+S shortcut
Depending on project size it may take from few seconds to few minutes to save the project.