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It sounds like you want to take a snapshot once in each workspace. That way, the next time you load it, it knows to return to the default configuration you set up.

You don't need to take a snapshot every time you use a workspace, just when there's some state you want to preserve your ability to come back to later.

The other alternative is to switch to another workspace with the windows you want to return to still open. OmniWeb is going to preserve the state you put that workspace into - including the state where all the windows have been closed. It's just putting things back the way it found them. :-)