Correct me if I'm wrong, but re-jetting is only accopmlished on carbed motors, followed by tuning, not re-mapping. Re-mapping is accomplished on fuel injected motors to accomodate increased fuel/air mixture.
There is a 'Tech Bulletin' concerning the re-flashing of the ICM on '04 and 05 XL's. Dated Oct. 20, 2004. EFI bikes have an ECM (electronic control module) which handles all aspects of the EFI and carbed bikes have no ECM only a ICM (ignition control module).
I don't believe the MoCo had a 'reflash' of the ICM to accomodate bigger jets. If you do have to replace your ICM, they probably will sell you one of the 'updated' models which won't require the 're-flash'.