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I'm a bit confused about what you're doing. If you install it on your Sandbox, then re-clone from Mac HD -> Sandbox, Parallels will be removed completely, unless you've installed it on Mac HD.
Software you install in Parallels is all inside Parallels' disk image, and isn't affected by the Sandbox at all. In fact, the Sandbox doesn't isolate anything about Parallels except for the application and its extensions, should you install it there.
Does that help?
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--Dave Nanian
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