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In the OmniFocus preferences, Data tab, what are the settings you have? My guess is that the missing items were refiled in a Miscellaneous single action list because they had a context assigned and that's all your settings required before a clean-up swept them out of the Inbox. That clean-up may have happened because you switched views coincidental to completing projects in your experiments.

Whenever items seem to disappear, use the All Items perspective to look for them.