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Given that no one else seems to have posted this problem this long after a release, I'm sure it's me missing something and that scores of you will jump in to show me the way.

When I set up Omnifocus on my Mac, I, having never used the software before, made some organizational decisions (eg, setting up projects and contexts) that I would now like to revise, but when I go to delete certain projects or contexts, I get a message that I would also be deleting some "hidden items." I'm reluctant to do that without knowing what those hidden items are.

The questions then: How do I make hidden items visible? Once visible, can I move them to another context or project and hide them again? (I'm assuming most of these are items that have been completed, put on hold, etc.)

Believe it or not, I've searched support for "hidden items" and am coming up with very little, certainly not the answers to my questions.
Go to the Perspectives menu and select "All Items". This will set the filters to show all items in your database.

Switching back to your other perspectives (or the default view) will then hide the exposed items again.

Hope this helps.

If you create a project with some actions, complete a couple of them, and then try to delete the project while in a view where you are only showing available or remaining actions (in other words, not showing the completed ones), you'll get this message. It's probably the most common reason for getting the message, though I wouldn't assume it to be the case and tell you to just go ahead and click OK!

If you use the built-in "All Items" perspective you should be able to do your cleanup without encountering this message.
Thank you! Worked just fine for me!
So completed items are considered "hidden"!

Omni really need to put an entry in Help that explains this! I searched and searched for some way to show "hidden" items.

I struggled for about an hour trying to find hidden items so I could delete a project. I got the warning that there were hidden items when I tried to delete the project. They weren't hidden, they were completed!

Ugh. I'll put this in as a feature request.
They are hidden from view if you don't have your view options set to show them. You'll get that warning whenever you try to delete a project and it contains some actions which are not being shown they aren't necessarily completed.

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