The record for the next day explains the reason, and there is no doubt that this was the copy of the Journal sent home.
The Queen's copy ends on 10th October.

The remainder of the Journal is taken from the Admiralty copy.) [Reports Sent Home from Batavia.] Wednesday, 24th.

Employ'd clearing the Ship, having a Store House to put our Stores, etc., in.

In the P.M.I went up to Town in order to put on board the first Dutch Ship that Sails, a pacquet for the Admiralty containing a Copy of my Journal, a Chart of the South Sea, another of New Zeeland, and one of the East Coast of New Holland.

In the morning the General, accompanied by the Water Fiscall, some of the Council, and the Commodore, each in their respective Boats, went out into the Road on board the oldest Captain, in order to appoint him Commodore of the Fleet, ready to Sail for Holland.