The attached script builds a 2.6.2 server with two JE backends. Upgrading to 3.0.0 apparently migrates both backends correctly.
DbDump shows the correct database names in both backends after the upgrade, e.g.
However the second backend's (ou=internal) id2entry is empty, as DbDump shows:
When you start OpenDJ it reports 0 entries in the internalRoot backend.
NB I repeated the exact same script this morning and both backends were migrated with all their data intact, so there may be some other factor involved.