I use the KS.cfg file to replicate my production hosts in our DR offsite environment. It occurs to me that we frequently will be using VMware Update Manager to update the hosts with new ESX4 updates (i.e. 4.0 to 4.1). Whenever this happens, I'm guessing that I need to copy the ks.cfg files again for my DR site. Is that true?
the ks.cfg file are the same for ESX 4.x, so you should still be able to find the ks.cfg on /root and using VUM shouldn't affect the contents of this file.
....with that said, update an ESX host and then compare the before and after, just to be safe.