The three references
The IMO number is kept and its check digit is verified whenever a record enters the system. Beside it sits the Manifest vessel identifier, twelve characters in three groups of four, for example 2010 CNHZ 7K4P: the year the keel was laid, the country it was laid in, the yard that laid it, and a final group assigned at random with a check character. A third reference is internal and is never shown to anyone.
Why the keel and not the ship
A ship's name, flag, owner, class, type, tonnage and length all change, several of them more than once. Where and when the hull was laid does not. An identifier built on anything else is accurate for a few years and then quietly wrong, which is how one vessel becomes two records and a fleet stops reconciling.
What it covers that the IMO number does not
Barges, small craft and anything else the IMO scheme excludes. Roughly 8% of rows in the archive carry no IMO number at all, and until now there was nothing to file them under.
Why the third reference exists
Build years are recorded wrongly, yards are misattributed, and both have to be correctable. The internal reference never changes, so a correction to what a vessel is rewrites the identifier the desk sees without disturbing a single record already attached to it.