This will have to be done from the command line as part of migration or upgrade install. We could also provide a small script so that users could do key/cert db migration without having to run the full blown migrate everything script. I will be removing the MIGRATE_DB operation from the securityOp (security.c) CGI - see CertMigrateConfirmPage.java.
The LIST_ALIAS op is going away as well.
The C code was fixed in admin server quite some time ago - what's the status of the Java code?