"I have my 4.0 partition first on the hard disk (1GB) and my 3.9 partition second. They have priorities 3 and 2 respectively. When I want 3.9, I load Media Toolbox in OS4 and change the priority of HD0: (the OS4 drive) to 1, and then reboot (remembering to hold down Ctrl-Amiga-Amiga for a few seconds so it flushes the OS4 out properly)."
eh? no need to change anything.
when you need to boot to 3.9, cold reset from AOS4 with CTRL+ALT+ALT .... enter in the earlySS without disabling anything, chose the 3.9 partition.... boot then enter another time in the earlySS and chose again th 3.9 partition.
AmigaOS4 pri 4
MOS pri 3
AmigaOS3.9 pri 1
Note- if you have IdeFix on 3.9, the thing is different ... another round to earlySS is required.