OS3.9 and OS4.0 in the same Amiga...

[zipper]

You have to tinker with boot priorities and boot from early startup screen to be sure that you get not the wrong patch loaded before the real startup happens. I have no problems with 3.9 and 4.0 lurking on different partitions.

[zipper]

I have a boot priority of 0 for DH0 (OS3.9) and DH1 (OS4.0) and 5 for DF0... which priorities do you have?

Don't remember exactly, but it depends on what you want to be the default behaviour. I think 4.0 is now higher than 3.9 so probably 1 against 0. If they are the same, the boot order depends of the partition names I think.

[zipper]

You need to get rid of resident patches, meaning at least 10 seconds power off.