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What happens if you've entered a total time by hand, and you change the project? Thinking about my projects and time estimates, it seems like no matter what the specified behavior (keep the manually entered time, clear the manually entered time, adjust the manually entered time by the delta of the change, take the new total time), it would be not what I wanted an appreciable fraction of the time.

That being said, I make essentially no use of estimated time in project mode, only in context mode when selecting individual actions to do. If I want a detailed estimate of a project's duration, I use OmniPlan, as there are likely to be dependencies and constraints not conveniently expressed in OmniFocus with a project complicated enough that eyeballing it isn't good enough. I do recognize, however, that buying OmniPlan isn't appropriate for everyone.