One of the key ways to interpret the list I have is to see which ships headed back the next year to Manila. In 1600, it seems four ships were sent, and it seems possible 3 made it, though there is some sketchyness about which ship did not make it.
An unnamed ship made it, in late 1600. In Jan 1601, two more pulled in to Acapulco. The names given are the Santa Maragarita, San Geronimo, and La Contadora. It seems like the Santa Margarita or the San Geronimo was the capitana, and another ship was the almiranta. Vizcano refers to his almiranta in 1602.
In the next year, the names of all these ships disappear, meaning they were all probably retired from the line.
The San Felipe was a Spanish galleon which, in December 1596, while en route from Manila to Acapulco, became shipwrecked at Urado Bay, on the coast of Tosa Province (Shikoku). It was towed into a bay and possibly wrecked intentionally by the shogun so that he could then loot the cargo. So that is where the San Feliepe II ended up.