Cost Adjustments in new NAV 2009 upgrade

We recently upgraded from 4.0 to Nav 2009 and it seems our cost adjustments were never correctly done in 4.0. That said, we now cannot close off past years in order to run cost adjustment for 2009(we run average cost) in the new Nav without running cost adjustment all the way through. The system will not allow us to block off past years without it running at least once. That said, its been running for 13 days on my test version. We had thought of deleting all transactions 2006-2008, but are not sure what that will do. Any suggestions?