I know sometimes you cannot stop waiting workflows before migrating although this is best practice.
If those workflows won´t contain any custom assemblies which won´t work in CRM 2011 then these workflows will migrate and continue to run in CRM 2011.
If you´ve custom assemblies you should check, if they are 2011 compatible otherwise your workflows won´t run.
And make sure while upgrading you´re mapping the same users. Otherwise your waiting workflow will run into errors.
You should backup your database and test your migration on a test environment before you´re migrating production environment.
Carsten Groth http://carstengroth.wordpress.com Microsoft Dynamics Certified Technology Specialist CRM Online 30 Tage kostenfrei testen – http://crm.dynamics.com/de-de/trial-overview