I have performed the preupgrade tasks on 6.1 and the preUpgradeHCStatus.properties file returns true.
Then I stopped the 6.1 instance. Moved the 6.3 jar into author and unpacked the jar. Then, I tried to migrate the repository to the latest oak by running
java -Xmx4096m -jar aem-quickstart-6.3.0.jar -v -x crx2oak -xargs -- --load-profile segment-fds
This command fails indicating that the source and the destination repositories are the same. Why would it fail when I use the recommended way to perform the upgrade from adobe documentation.