Your options are using a parameter set or a parameter file.
1) Parameter file: the scheduler could call a script that takes the jobID and inserts it into the top of the parameter file under the global section. This still leaves the base file intact but gives you the dynamic piece you need. I would would copy the base file into a temporary file, insert the jobID into the temp file and then throw away once done/throw away after X amount of time/runs.
2) Parameter sets: This is the approach I would go with. Par sets allow you to configure the same parameters as a file but you see them in the developer tool as well as you can infacmd's to create, add and update entries in the sets. So you can have ActiveBatch pass the jobID to a script that calls the pmcmd to update the jobID for a parameter and then pass the par set to the workflow.
Hope this helps.
Thanks very much for your response. We tried approach #2 and it works like how we expected.