The decision to move the shop order to the new revision is not really an IFS decision, it is a design decision based safety, longevity, or inventory concerns. Once the decision is made for which orders are affected and need to be up-revved. I find it best handled with the shop order at Planned or Released, then the shop order can be updated using the RMB from the header for the new revision.
If the shop order is in a started status, then it depends on how extensive the change is, it may be necessary to manually unissue some parts and update the material tab manually, or it may be more efficient to un-issue the entire shop order, up-rev, then re-issue the parts. It is hard to say the best practice because it depends more on your manufacturing and engineering decisions than IFS functionality.