just uninstall and install the package, its just a script that copy's files on installing the script and after replacing the content of the root file system the files are missing
a complete new/big version like 6.1.1 and 6.1.2 replaces the content of /dev/md0, so modificacions like changed scripts, changed configs - like max. disks
if you open the *.pat with 7zip you will find a hda1.tgz, the content of the root file system aka the new dsm version
so if you have modifyed the synoinfo.conf you also have to redo the changes
would be intresting to know what experiance people have that user more then 12 disks after such update as the count of disks is restet to 12 and the actual raid in place contains a more disks (i'd expect a crashed raid after update if you boot with the new version without modyfiening it before the first boot)