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I'm not positive about your goals, but it sounds like Union might not the best technique. Since the 2 paths are not connected, or anywhere near each other, and Union needs to make them into a single object, Inkscape has to do some guessing, based on the info provided in the origial paths.
If you need the 2 paths to be subpaths of the same compound path, I'm thinking Path menu > Combine might be the best technique. Nothing will change, except combine the 2 paths into one.
If you try that, and it's still not what you want, would you please describe what you want to do? I can't quite see what's happening with your screenshots. The result of Unioning the 2 objects that are selected in the "before" should not be bigger than the original 2 objects, which is what it looks like in the "after". And I don't understand why objects that appear not to be selected are somehow affected by the Union command. We may need to see the SVG file, but let's go one step at a time.
Let us know if Combine works
