And the reasons to throw out the baby with the bathwater versus not:

There are two things in the database that you might care about:
-UI Customizations
-Running workflow states

The first one is obvious. The second is more subtle. Some implementors use workflows as timers, with an approval activity at a specific timeout to allow the process to continue. If you have many many of these workflows in a running state, you should upgrade your database so that you don't lose the running workflow states. If you don't implement in that way, and therefore there aren't large numbers of workflows awaiting a timeout, then check workflow status, wait until all the running workflows are completed, and it's way easier to start from scratch. The upgrade process for the database is fraught with mines to step in (all of them can be worked around, most will require an SR if you haven't been initiated). My clients have the battle scars here to prove it.

-Rob