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Most of this has started to get cleaned up around the 2V2.2/2.2.1 timeframe, but the specifics vary and it's less useful to try to explain every last combination than to document the general things to be careful about. If you're starting from an official 2V2.2.1 package, you can consider anything that doesn't work as intended during an upgrade to be a bug worth reporting.
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The main area of trouble is related to the handling of the /etc/init.d/shibd script, which until recently was improperly controlled by the SP package. In addition a bug was introduced in the 2V2.1 SP that results in problems when upgrading from that version.
If you're upgrading from an older package and 2V2.1 isn't involved, the process is believed to be safe in this respect. On versions of Red Hat with RPM 4.4. or newer, these problems are believed to be worked around, so upgrades should also be safe in that case. That includes Red Hat 5, but does not include Red Hat 4. It also doesn't include cases where unofficial packages on other platforms like SUSE are involved.
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This "advice" was enforced by simply blasting your changes by re-copying the original over top of your version during an upgrade. This has now been corrected (in V2.5) by marking the file as a configuration file to replaceprotect, which ensures your version will be renamed out of the way and preserved for youleft in place.
Unfortunately, that only occurs when upgrading from a very relatively recent version, because prior package versions don't do this may remove the file when they remove themselves during upgrade. So to be safe you should probably back up that file yourself if you have anything important in it.
Process Restarts
Until recently, the package upgrade process did not properly restart the Apache and shibd processes after an upgrade, which leaves the system in an unstable state and can exhibit runtime problems, particularly if one process was restarted but not the other. This should be corrected in 2V2.2.1, but it's something to watch for.
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