Hi,
Important questions to ask,
1) did you version workflows so you can tell which version each workflow is?
2) are you using persistance? Do you have access to currently running versions.
Generally, to upgrade your running instances here what is you would do.
1) Create an app to load your instances from a persistance store
2) Apply the changes to update your workflows using the api's available (workflowchanges)
3) Save the instances back to the persistance store
Voila, the next time the workflow is loaded to execute, it will be upgraded.
Note that we restrict you to modifying workflows that are in the currently idled / created / suspended states. So this assumes your currently running workflows that do go into the idle state or that you put them into the suspended state.
Here is a good blog on how to play with the feature.
http://blogs.msdn.com/markhsch/archive/2005/09/23/473373.aspx
Thanks
Sung Hon