Based on the number of running process instances with the incorrect template, and the probability that the particular transition is triggered in the process, we were able to estimate the number of instances that would terminate abnormally. Fortunately the number (both the estimated and the actual) turned out to be small (around 10), so that the business impact was quite low. Nevertheless this was a very frustrating experience because you can only sit and wait until another process instance becomes corrupted. It was not possible to proactively fix the running instances because MQ Workflow didn't allow you to migrate running process instances to a new version of the process template (and recreating these instances using some custom built ad hoc tool was far too risky).
Ever since that incident, whenever I meet somebody who happens to be (or pretends to be) a specialist in BPM, I always ask the question of how to address this type of issue. I even asked that during a IBM training session on WebSphere Process Server. I never got a satisfactory answer. It was only when I worked for Accenture that I discovered that some smart guys in their labs had studied that issue and come up with a pattern to solve it. If I remember well, the pattern somehow suggested to implement a single business process using three different BPEL processes that would then interact together. Even if the overall process is long running, one of these BPELs would only be short running so that it could be replaced by a new version at any time. Obviously this type of pattern far from optimal since it is expensive to implement and tends to further increase the gap between the process designed by the business analyst and the BPEL executing this process.
Recently IBM announced the release of WPS 7 and the announcement mentions the following new feature: "Deliver migration of running processes to new process model versions". If this is really what I think it is (and if the IBM people are able to deliver what they promise, which of course they have always been ;-), then this will be a major step forward.