What is in OS3.5 or 3.9 that isn't in 3.1?

[amigakit]

One of the most important updates in OS 3.5 and 3.9 is Large Hard Disk support-  standard OS 3.1 does not work with hard disks above 4Gb and even with patches cannot report large hard disk capacities correctly and perform a full format.

OS 3.5/3.9 has a new FastFileSystem, fixed HDToolbox, fixed scsi.device and updated Format tool. IMHO, very important if you want to use a new hard disk in your Amiga.

[amigakit]

Unfortunately OS 3.1 does not support 64-bit addressing in ROM so even with third party patches, you still cannot do a full format with Workbench - also the Workbench will fail to correctly report the capacities of the larger hard disks.

Only 3.5/3.9 does this correctly as it patches the Kickstart ROM.

[amigakit]

I was referring to OS3.5/3.9's ROMUpdate file that Softkicks a 3.9 ROM from Setpatch to update the scsi.device etc

When large hard disks are used - Workbench 3.1 always reports incorrect geometry in 3.1 (Window Title bars etc) regardless of third party patches.  The ROMUpdate in 3.5/3.9 resolves this issue.  Likewise the latest HDToolbox and Format tools has fixed support for the geometry problems.