I think the best option would be if someone created a nice GUI util that allows you to swap the boot priority back and forward between which partition you wish to boot from.
That way you could click on your OS3.1, OS3.9 or OS4 partition as your default boot partition then ether click a reboot button or reboot manually.
That way when reboots for setpatch, IDEFIX etc would not be a problem.
Then next time you want to change with AmigaOS you want to boot you would just run the util again and click on a different bootable partition.
