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If I understand the question, I may have a possible solution.

To create a to-do in OF from an e-mail, use the clipping services (to activate check preferences and install the clip-o-tron 3000 at the bottom of the menu). I've set the keyboard short-cut to shift+command+comma.

So, highlight the mail, hit your short-cut, and fill out the necessary info in the pop-up window - project, context, start date, and end date.

Then, I use Mail Act-On by Indev to send the e-mail to an archive folder. In my case, I've programmed a keyboard shortcut for that. You can send it to another folder (a folder named "waiting on" or "action needed", if that fits your work flow better.

This workflow in two keyboard short-cuts gets your e-mail out of your inbox (in-box 0) and creates an entry in OF. The original message link in your your OF entry will open the original e-mail, even if you move it to another folder.

Hope this is useful.