Prey, is there any drawback if converting the dual_iso unprocessed cr2 to dng (non-lossy of course) and *then* put them through cr2hdr?
I actually do that. For archiving, I delete the dual ISO output files and keep the unprocessed dng's.
On Windows, be careful because they have the same extension, so the unprocessed one will probably get overwritten. On Linux, Adobe DNG converter outputs lowercase dng's, and cr2hdr outputs uppercase DNG's => no conflicts.
To solve this on Windows, one way would be to rename the unprocessed .dng back to .cr2, since dcraw doesn't care about the extension. Ugly, but gets the job done.