The Yosemite installer estimated times will be inaccurate. Part of the upgrade involves moving /usr/local out of the way. The process of moving those files back after the upgrade is done one file at a time and seems very slow. - Jim Lindley
I can understand why an installer moves stuff around, but this seems dangerous. Especially considering for example the following:
By default, Kerio Connect is installed to /usr/local/kerio/mailserver. Now you can change the location. - Kerio
I manage a Kerio mailserver and luckily our user's data doesn't live in that default location anymore. Imagine updating such a server and waiting for the server to migrate 500GB of emails at 10-20kb per file from one place to the other at a ratio of one file per movement.
The upgrade would take days.
So my advice: get a new Mac mini, install OS X Yosemite from scratch, install Kerio Connect and import your existing data. You'll safe a lot of time, and your Kerio database gets optimized at the same time.