You're getting confused between save and publish.
If you use save, it saves a livery. If you use save again, it'll save over that livery.
Save as will allow you to save the livery with a different name so you can have 2, (or more) similar liveries without having to start from scratch.
These appear as files you can open in the livery editor.
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If you save it and publish it so you can use it, it will be in the livery editor and will also appear in your collection. If you save and publish again, there will still only be one livery in the editor, but there will be 2 in your collection. Repeat again, and there will still be one in the livery editor, but 3 in the collection.
One livery can be published many times to give you many versions of it in your collection.