Based on other threads, I double-checked that the notations near the JP-1 pins do say JP-1, not JP-1.1.
I used RM and loaded up the "Sony DVP-NS355 and DVP-NS585P" device upgrade from here. I first used IR to upload that device to a modified URC-6131 which worked beautifully. The 6131 controls the new DVD player just like I hoped it would.
I then changed the remote in RM from the URC-6131 to the Altas using this RDF: SA_7SA_7 (Atlas DVR-PVR 5-Device).rdf
The auto-layout for the keys on this remote looked fine, so I copied the output to IR and uploaded to the Atlas. Unfortunately, the Atlas is not controlling the DVD player.
If I Download From Remote using IR, the device is definitely there. Another symptom is that I can no longer assign the published Sony DVD device code using the remote: (DVD, Hold Set for 5 seconds, 0533) blinks once instead of twice.
Is there anything I can do to debug this further?