I did the upgrade on my ispconfig 3 systems like this:
1) Debny all config file chnages except of the mysql my.cnf file.
2) If mysql does not work after the update (I had this on my systems), just reinstall it with apt like this:
apt-get install --reinstall mysql-server mysql-client
This reinstall will just force an update on the binaries and does not remove existing databases.