What I did to test in the end was to create a small virtual machine and install the packages from the existing setup. I then copied over /etc/nagios. I updated to the newest nagios and ran a nagios -v /etc/nagios/nagios.cfg to see what broke. For our setup we had customized things in a way which 'worked' in previous versions but didn't in the new version. I fixed those up and then edited my nagios.cfg differences into the nagios.cfg.rpmnew so I got the additional configs that the new version wanted.