The National Archive of Indonesia published on her website tables of contents of the so-called Daghregisters (Daily accounts) of the Castle Batavia. Unfortunately they are in Dutch. In those tables you can find for instance information about the ships arriving at and departing from Batavia (nowadays Djakarta). I extracted the movements of the Portuguese ships and vessels owned by the E.I.C. The Portuguese names are phonetically written. The dates mentioned below in the text are the register dates.
Anapourna, yacht, arrived at Batavia coming from Manila 4 March 1685
Nossa Senhora de Monseratte, small ship, arrived at Batavia coming from Macao 31 December 1685, as Monserrate departed Batavia towards Macao 22 May 1686, news of the wrecking of the Monseratte in Sunda Strait 26 May 1686
Nossa Senhora de Quia en Zint Anthonio, chialoup, arrived at Batavia coming from Siam 13 December 1686
Nossa Senhora de los Milagris, ship, wrecked off the Aguilles 29 July 1686
Nossa Senhora dos Milhados, ship, wrecked off Cabo Palco, 5 crewmembers allowed to travel to Malacca 27 September 1686
Nossa Signora de Rosario Grande, small ship, arrived at Batavia coming from Macao 3 March 1685, identical with the Nossa Signora de Rosario towards Macao with a priest of Toncquin 14 June 1685?
Santo Anthonij, departed Batavia towards Mocambique 17 July 1685
Sint Catharina, small yacht, arrived at Bantam coming from Madras 23 December 1686, her captain Bernardo Mendes was allowed to go on shore for some days 27 December 1686
