I've tested this myself again a few weeks ago - with a straight-up Smart Update restore, the recovery partition was maintained as expected. I don't know why your recovery partition was removed - as I've said previously, we copy ONLY to the selected partition.
I wish I could reproduce the problem, but I haven't yet been able to.
Note, though, that there's no real "fear" involved in losing the partition: reinstalling Lion will bring it back if "lost"...
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--Dave Nanian
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