Yes, as we use cPanel internal migration scripts, MySQL and it's data will be transferred. The /etc/my.cnf file is not transferred by default, but we can move this for you.
We had your support team migrate the website over and we ran into too many issues trying to get the software running correctly and decided to stay with the Hybrid we have already with knownhost. It was a time factor for us right now. We will be trying again after the holidays with a clean software install.