OK, I'm still waiting for my copy of OS4. But, my machine is already prepped for it. I don't know the first thing about kickflash (yet).
I don't see why OS4 should affect any other partitions/drives/etc. What filesystem(s) do you use?
I mean, I can totally corrupt a partition and 3.9 could care less. As long as the 3.9 boot partition has priority, it boots.
I do have problems occasionally with the kickstart that 3.9 uses getting corrupted (due to a bad memory access or something) and I can't warm boot at all then. But, all is well after the next cold boot.