OS 3.9 CD has all the same files, with a few exceptions, only they have been updated and generally improved, so you get a better feel, useability from Workbench.
So OS 3.5 CD is an unnecessary install.
If you have WB3.1 then you will see a big change to WB3.9, especially if you have never installed NewIcons, which was a hack for WB3.0 and WB3.1.
If you have an IDE board installed, make sure you have the original floppy install disk, as you may require the keycode that is used to install the hardware/software, as the keycode, written usually on the floppy disk. This is different with the Elbox boards that have an in-built file/code in the hardware that recognises the software being used. The IDE boards may refuse to work on the 3rd and 4th channel if you don't have this information.
If there are any other keyfiles on the Workbench partition then don't forget to save those as well, quite often in the "S" directory, but sometimes in "Devs" or elsewhere! such as the programs directory, like IBrowse does.
You should be able to just copy each partition of the current Workbench and any other partitions that are on the hard drive that came with the system, onto another formatted, similar sized/partitioned hard disk to keep as a backup without any problems. Just drag and drop the files, though you may need to copy manually the disk.info and .info file on a hard disk with that file on it. Use Directory Opus to do so, or any other filemanager you use to achieve this and you will see the .info files as well, in the list windows.
If you have no spare hard drive, then why not consider backing it all up to a CDR/RW, if you have a CD writer for your Amiga, using the now free fully useable MakeCD, which you will need to pick up the generic key licence from the MakeCD website.