Sorry to be so dense but are we talking about the 2632 resident module? Because AFAIK that goes away on the next reboot. The 2632 isn't autoconfig so you have to give the 2632 command on every boot.
I don't understand what you mean by "after you install the Amiga OS ROM update". Do you mean I should now remove the NOROMUPDATE option from SetPatch? I assume we'd just go back to the previous state where adding the 2632 causes all commands to fail with error 41.
Yes, we are talking about the 2632 resident module and no, it does not go away after the next reboot. You will have to power down (cold boot) to remove it.
The observed behavior with using the OS 3.9 ROM update was supposed to be an "Auto reboot". Hence, I saw no need to explain it any further. Now, there are 2 possibilities here:
1) 2362 command before Setpatch = resident module conflict with OS 3.9 ROM update auto reboot
2) 2362 command after Setpatch = resident module conflict with next user reboot
So either way you still have the problem, it just a matter of when.