Yahoo! Soon we will be able to modify running BPEL instances.
Ever since I started to work with BPEL, we ran into the problem that when you upgrade a BPEL process to reflect a changed situation, you will have to think about how to handle the already running instances. There were not many options: you either let them run their course or aborted them to restart them with the new version.
In our case we had a lot (15.000+) of rather long-running processes (up to 14 months). So you can imagine both options were not very attractive. Yesterday I had an upgrade about the upcoming Oracle SOA Suite 11g. The very good news was that in Oracle BPEL 11g you are able to modify already running instances. That is very very good news indeed.
It will have some limitations however, but that has more to do with the structure of the process. You will have to think about where you will allow any modification on running instances.