I updated through apt-get update. Didn't really pay attention if mailscanner was also updated. But I followed the guide to correct the symlinks and checked those files in /opt/MailScanner/lib/MailScanner/CustomFunctions according to the upgrade guide and all .pm files contain the correct database credentials.
Everything also seems to be working fine as is Baruwa. Only problem is that the processing stops after a few days and mailscanner keeps restarting, only way to get the queue to process is to reboot. Yesterday this happened exactly around 00:00 hours on both spamsnakes I built and I also noticed a lot of mailscanner (defunct) processes through top when the problem arises. Before the update of baruwa and ubuntu it was running fine for months (very stable)
I tried troubleshooting but this is a tough one to crack.