I don't know about OS3.5, but I installed OS3.9 on my fairly basic A2000 (KS3.1, SCSI HD & CD ROM, 8 MB RAM expansion) over the existing OS3.1 installation.
The only problem I had was that after installing the supplied "updated" drivers for my Cybervision 643D graphics card it cratered and went into a software error/reboot loop. I've been informed that this was because I should have used the original disks that came with the Cybervision card (not the updated ones), but I haven't got around to reinstalling yet.
