The process for restarting migration from NXRM2 to NXRM3 as described in the upgrade procedures document https://help.sonatype.com/repomanager3/upgrading/upgrade-procedures#UpgradeProcedures-RestartinganUpgrade requires that the user deletes the NXRM3 data directory. This has the unfortunate side effect of deleting all of the customizations that were applied. After I deleted the data directory, and restarted nexus 3, I first had to reconfigure LDAP, and create the additional blob stores that I had defined. The application context path defined in $DATADIR/etc/nexus.properties is also lost.
It seems that the only customization that was preserved was our Nexus Pro license.
It should be possible to restart repository migration without resetting all of the configuration that has taken place. For example, in NXRM2, it is only necessary to delete sonatype-work/db/migrationagent directory to restart migration. For NXRM3, there should be a similar approach that preserves the rest of the configuration.