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As Curt noted, this is almost certainly an issue with a filter or focus being set. If OmniFocus did lose any of your data, that would be a show stopper -- please let us know as soon as possible how to replicate it if so. If OmniFocus convinced you your data was gone via poor UI, that's also a serious bug, so let us know about that too, if that's the case.
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CTO, The Omni Group