Solution:

1º) Get a fleet into a port, and the other fleet nearby.
2º) Build a "Navis Oneraria" on the same port, so that the oneraria appears attached to the existing fleet.
3º) After you do that, you should have a fleet with a navis oneraria and your old, experienced ship. Select the experienced ship, and move it to the other desired fleet that was standing nearby.

Repeat until you have merged all your fleets.

Cheers!