Currently, engine-upgrade will overwrite VDC_Options during 3.0 -> 3.1 upgrade with default values. The upgrade should honor non-default settings and not change them.
the option which will be overridden with 3.0 -> 3.1 upgrade (in case user changed the defaults) are: "CABaseDirectory":["/etc/pki/ovirt-engine", 'text'], "keystoreUrl":["/etc/pki/ovirt-engine/.keystore", 'text'], "CertificateFileName":["/etc/pki/ovirt-engine/certs/engine.cer", 'text'], "CAEngineKey":["/etc/pki/ovirt-engine/private/ca.pem", 'text'], "TruststoreUrl":["/etc/pki/ovirt-engine/.keystore", 'text'], "ENGINEEARLib":["%s/engine.ear" %(basedefs.DIR_ENGINE), 'text'], "CACertificatePath":["/etc/pki/ovirt-engine/ca.pem", 'text'], "CertAlias":["engine", 'text'], "TruststorePass":[basedefs.CONST_CA_PASS, 'text'], "keystorePass":[basedefs.CONST_CA_PASS, 'text'], "SSLEnabled":[ "true", 'text'], "ScriptsPath":["/usr/share/ovirt-engine", 'text'], "SysPrepXPPath":["/etc/ovirt-engine/sysprep/sysprep.xp", 'text'], "SysPrep2K3Path":["/etc/ovirt-engine/sysprep/sysprep.2k3", 'text'], "SysPrep2K8Path":["/etc/ovirt-engine/sysprep/sysprep.2k8x86", 'text'], "SysPrep2K8x64Path":["/etc/ovirt-engine/sysprep/sysprep.2k8", 'text'], "SysPrep2K8R2Path":["/etc/ovirt-engine/sysprep/sysprep.2k8", 'text'], "SysPrepWindows7Path":["/etc/ovirt-engine/sysprep/sysprep.w7", 'text'], "SysPrepWindows7x64Path":["/etc/ovirt-engine/sysprep/sysprep.w7x64", 'text'], "ConfigDir":["/etc/ovirt-engine", 'text'], "DataDir":["/usr/share/ovirt-engine", 'text']
I noted this issue in the "RHEV 3.0 to 3.1 Upgrade" kbase article (https://access.redhat.com/knowledge/articles/269333). For now, the article notes that any changes to these values are overwritten.