The National Archive of Indonesia published on her website tables of contents of the so-called Daghregisters (Daily accounts) of the Castle Batavia, HR no. 2519. 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 ships and vessels owned by the E.I.C. The dates mentioned below in the text are the register dates. See also on this weblog the notes dealing with cargo capacities and individual ships.
Andromeda, arrived at Batavia coming from Bantam 3 November 1699
Bije, small yacht, mentioned 25 November 1699, arrived at Batavia coming from Sunda Strait 29 November 1699
Boswijck, departed Batavia towards Malacca 16 November 1699
Casteel Batavia, ship, arrived at Batavia coming from the Netherlands 1 November 1699
Donkervliet, ship, arrived at Batavia coming from the Netherlands 1 November 1699
Eemland, yacht, departed Batavia towards Malacca 29 November 1699
Geelvink, small yacht, arrived at Batavia coming from Bengal 19 November 1699
Liefde, ship, news dealing with her arrival in Sunda Strait coming from the Netherlands 11 November 1699, arrived at Batavia 13 November 1699
Oosthuijsen, fluyt, arrived at Batavia wit letters from Tagal and Cheribon 15 November 1699
Oostersouburgh, ship, news of her being sighted at Poulo Chinco 1 November 1690, arrived at Batavia coming via the West Coast of Sumatra from Suratta 18 November 1699
Oostvoorn, ship, arrived at Batavia coming via Palembang from Malacca 2 November 1690
Overrijp, fluyt, arrived at Batavia coming from the Netherlands 5 November 1699
Peperthuijn, small yacht, departed Batavia towards Palembang for a cargo of pepper 26 November 1699
Pool, frigate, departed Batavia via Malacca towards the West Coast 10 November 1699
Prinslant/Princeland, ship, news of her being sighted at Poulo Chinco 1 November 1690, arrived at Batavia coming from Persia 12 November 1699, destined to collect a cargo of pepper at Bantam 24 November 1699
Purmer, arrived at Batavia coming from Japara 6 November 1699Schelde, departed Batavia towards Cheribon with a cargo valued ƒ 352:17:00 4 November 1699
echt, fluyt, arrived at Batavia coming via the West Coast from Bengal 30 November 1699
Voetboogh, fluyt, arrived at Batavia coming from Japan 30 November 1699
Wind, yacht, departed Batavia via Malacca and Ceylon [Sri Lanka] towards Mallabar 3 November 1699
Woggenum, ship, arrived at Batavia coming via the West Coast from Chormandel 6 November 1699
Andromeda, arrived at Batavia coming from Bantam 3 November 1699
Bije, small yacht, mentioned 25 November 1699, arrived at Batavia coming from Sunda Strait 29 November 1699
Boswijck, departed Batavia towards Malacca 16 November 1699
Casteel Batavia, ship, arrived at Batavia coming from the Netherlands 1 November 1699
Donkervliet, ship, arrived at Batavia coming from the Netherlands 1 November 1699
Eemland, yacht, departed Batavia towards Malacca 29 November 1699
Geelvink, small yacht, arrived at Batavia coming from Bengal 19 November 1699
Liefde, ship, news dealing with her arrival in Sunda Strait coming from the Netherlands 11 November 1699, arrived at Batavia 13 November 1699
Oosthuijsen, fluyt, arrived at Batavia wit letters from Tagal and Cheribon 15 November 1699
Oostersouburgh, ship, news of her being sighted at Poulo Chinco 1 November 1690, arrived at Batavia coming via the West Coast of Sumatra from Suratta 18 November 1699
Oostvoorn, ship, arrived at Batavia coming via Palembang from Malacca 2 November 1690
Overrijp, fluyt, arrived at Batavia coming from the Netherlands 5 November 1699
Peperthuijn, small yacht, departed Batavia towards Palembang for a cargo of pepper 26 November 1699
Pool, frigate, departed Batavia via Malacca towards the West Coast 10 November 1699
Prinslant/Princeland, ship, news of her being sighted at Poulo Chinco 1 November 1690, arrived at Batavia coming from Persia 12 November 1699, destined to collect a cargo of pepper at Bantam 24 November 1699
Purmer, arrived at Batavia coming from Japara 6 November 1699Schelde, departed Batavia towards Cheribon with a cargo valued ƒ 352:17:00 4 November 1699
echt, fluyt, arrived at Batavia coming via the West Coast from Bengal 30 November 1699
Voetboogh, fluyt, arrived at Batavia coming from Japan 30 November 1699
Wind, yacht, departed Batavia via Malacca and Ceylon [Sri Lanka] towards Mallabar 3 November 1699
Woggenum, ship, arrived at Batavia coming via the West Coast from Chormandel 6 November 1699