Domains created in custom-path other than as-install/domains directory are not upgraded directly while upgrading from Application Server Enterprise Edition 8 to Application Server Enterprise Edition 8.1.
When running the Upgrade Utility and identifying the as-install as the source installation directory, the upgrade process upgrades only those domains that are created under as-install/domains directory. Domains created in other locations are not upgraded.
Before starting the upgrade process, copy all the domain directories from their different locations to the as-install/domains directory.