How to solve this problem (in WF4):
I create a workflow in xaml and start several instances of it, I have a persistancestore and all workflows persist on a bookmark
It's not so much an issue with Windows Workflow as it is the SQL persistence service. You could create your own persistence service that can handle this situation, either by supporting conversion of the old workflow into the new workflow or something more abstract, like a persistence service that serializes as XML/JSON, something that might more easily support deserialization of one version as another version.