For those who don't like to read stories, here's the extract:

Today I got a notice from ESET Remote Administrator Console about new updates being available and a prompt to get them from the website. I downloaded two new executables (Server and Console) for version 4.0.138.0, went to our ESET server and started the update. I was quite surprised it did not say anything about some version already installed on the system. It really appeared to be a clean install from the first 2-3 wizard screens, it even prompted for a license key.

Thanks to Google, I found this forum discussion, where ESET moderator explained it is exactly how update works - you do a clean install over your current version. To be safe, I made a shadow copy of the virtual machine, and backed up ESET database to a dump file. After that a clean install was attempted. I just went Next...Next...Next hoping to preserve the old configuration. I supplied a license file, and did not set a password, where it said to do so (or it is assigned blank). On the update parameters screen, it automatically assigned username and password, and at this point I figured I am not really doing a clean install. In the end, it warned about ESET server needing to close, confirmed that, and got a working version soon after that.

No configuration was changed, even the password was not blank, but our good old password instead.