Cleaning Up – Where Does It Go?

The easiest way is probably to drag the items from the old one to the one OmniFocus is now using.

If you really really really didn’t want to do that for some reason, I can imagine a solution involving moving your database back to your OmniFocus 1 folder, tweaking the preference there and then copying it back, but I have not tried this. (aka Proceed at your own risk!)

If it’s really important to you to swap it back to the old folder, I’d be quite curious to understand why.