You can normally see if the defaults have been changed when the APAR ID field is ‘CHGDFT’ and the User modified is a 1. If the user modified is a 1, then something has changed and I would recommend copying the command to another library before your upgrade.
Once you’ve done the upgrade you should compare the copied commands and see whether there is really a difference (it’s possible that someone/some program has done a CHGCMDDFT with the same defaults that were already in place, thus marking the command as changed).
If you need to change a system object, you should really copy it to another library which you keep above the system libraries in the QSYSLIBL system value. The new way to do this is using ‘proxy’ commands, if you can you should convert to using this method.
By the way, are you sure it’s V5R6 that you’re upgrading to? I thought that after V5R4 the next release was V6R1.