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The warning is basically to be careful: if you don't use the right options, and don't back up the base volume first (if you make a mistake), you could lose data. But Sandbox users are typically pretty sophisticated.
If you Smart Update the base drive from the Sandbox (using "Backup - all files", not the Sandbox scripts, as you know), the OS would be updated to the one from the Sandbox, so bootability on the base drive is more a function of the Sandbox itself...
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--Dave Nanian
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