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OmniFocus is a database, whereas OO3 is a document editor.

When you 'clear' the checked items in OmniFocus they disappear from the current view but are still in the database.

In OO3, you can run a simple script like:

Code:
tell application "OmniOutliner Professional"
	tell front document to select (rows where state is checked)
end tell
which will select all the checked rows in the open document. Whether you then cut and paste them to an another document, or simply delete them, is up to you.

(If this moving or deleting were a regular requirement, it could also be scripted and assigned to a keystroke or a button on the toolbar).

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