Well, not quite to late to put in this piece of information and might help you all who are trying to upgrade from NAV 3.6 version to NAV 2009. For the past few days I have been trying to estimate the way forward to upgrade a NAV 3.6 database to NAV 2009.
The above seems possible and many of you have even succeded in the same, simple steps when followed will help you acheive this.
Upgrade the objects in NAV 4.0 as win your client DB, upgrade the data using the upgrade toolkit and then start your upgradation of objects in NAV 2009, again use the upgrade toolkit for NAV 2009 to upgrade the data to NAV 2009. Make the db live. Simple....
Now think of a scenario where a DB is present in NAV 3.6 IN version and you want to upgrade to NAV 2009 W1, think..
I will let you know my findings soon..