Not sure I am completely following...Are you looking for the latest version of each referenced file? If so the Convert Task is the tool you are looking for.
Otherwise you may consider creating the pdf (with the convert task) as the referenced files go through the workflow, and including the revision value as part of the file name.
Little bit hard to explain, but let's try..
We don't use versions in production, only revisions. Approving creates revisions which creates pdf's. We have a tool that batch exports all PDF's for the selected structure, but it doesn't read the revisioned structure. Instead it uses the latest versions. So if somebody creates new revision which, when checked in, creates new version, the PDF is not exported for that drawing (because PDF is created only when revision is born)
So what we need is way to batch export all pdf's for the structure that was really used when the main assembly drawing revision was for example "0" and all other drawings were also revisioned = approved.
I understand that EPDM is more like DMS than PDM, but it's quite stupid that the only way to get all pdf's for the production revision is to collect them by hand from...what ever folders they might be.
I don't know if we can modify the current batch export tool (is it just code that we can change or is it dll or something) to work this way...have to check that out tomorrow.