We are having the same issue, music.xml files will open a new project in Cubase. How does one import into the current project?
[edit] This is the answer:
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import your music.xml file from within Cubase Pro (you will have to navigate to the music.xml file, press Enter, then choose the place, where the new project should be saved, then press Enter again). A new Cubase project will be produced and saved at the chosen place.
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Open the Cubase project you are working on (or make it active, if it is already open), go to File → Import → Import Tracks from Project. Navigate to the prior saved project and press Enter. This will give you a window with a lot of options. By default the tracks from the other project will be imported into new tracks of your active project.