Upgrading Workflows in an existing SharePoint site can be very tricky. Just copying in a new version is not the best practice. Depending on what changes were done to the new version of the assembly SharePoint may end up having trouble re-hydrating (deserializing) the currently in-progress workflows.
Here are some excellent articles I found recently on how to properly implement versioning, its potential pitfalls and how to overcome them:
- http://msmvps.com/blogs/theproblemsolver/archive/2008/09/10/versioning-long-running-workfows.aspx
- http://msmvps.com/blogs/theproblemsolver/archive/2008/09/11/versioning-long-running-workflows-part-2.aspx
- http://msmvps.com/blogs/theproblemsolver/archive/2008/09/16/versioning-long-running-workfows-part-3.aspx
- http://msmvps.com/blogs/theproblemsolver/archive/2008/09/22/versioning-long-running-workflows-part-4.aspx
Another alternative approach which I think is also a good solution:
