MySQL upgrade cannot make any problems for your database if its done in a proper way. You should ensure that the upgrade process takes care of making changes to the databases as per its requirement and it takes care of fixing all problems.
We have upgraded MySQL Server version couple of times but none of our customers complained as we give advance notification and the upgrade is done by our expert system admins.
Cpanel has simplified upgrades for mysql, apache, perl, php, Fantastico and many other inbuilt softwares and all you need to do is keep yourself updated with what new features have been implemented with new release of cpanel.
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