Hello David,
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While Rumphius was indeed in Batavia for for 4 years from 1653-7, where he began as a midshipman and ended as an engineer and ensign,
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There are quite a few conflicting dates regarding Rumpf's biography - I'm not sure if it is feasible or necessary to dig into this? It seems that he left for the Moluccas in 1954 at the latest (the recent account by Baas & Veldkamp 2013 stating him leaving Batavia "after some weeks" only!). Despite him (possibly early on and definitely later on) staying connected to Bataviaasch VOC circles, it seems fair to state (judging from the corpus of his notes) that Java was not his major playground and we may have to accept it being more likely for him to include some erroneous info, too.
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i am not convinced that he began his ethnographic studies until he left the service to continue as a civilian employee of the VOC.
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There are also ample natural history notes from his earlier "stay" in Portugal. He had a high-level education and obviously was one of those homo universalis (Universalgelehrte, i. e. scientists interested in just about everything) of days past. Thus, it seems very reasonable to assume that he was always collecting data...
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He didn't begin his serious studies of the flora and fauna of Ambon until 1662, 5 years after his arrival there. The book linked above wasn't published until 1705, 3 years after his death.
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It's a wonder that (most of) the manuscript got compiled as well as survived at all: author becoming blind, earthquake & tsunami, ship sunk in transit, VOC declaring it a trade secret...
BTW, I'm fairly sure that he started observing and collecting right after his arrival - arguably, it will be difficult to ascertain how much time he could spend while serving for the military arm of the VOC (which he left in 1657 and settled down as a VOC merchant).
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His masterwork, Herbarium Amboinense, wasn't published until 39 years after his death in 1741. What a shame not to have seen all his efforts come to fruition in his lifetime.
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It was not unusual in those times to have the magnum opus published posthumously, especially with many visiting the tropics passing away within a few years. FWIW, he already got recognised as one if not the leading authority on tropical plants during his life time; I guess this helped to face the many adverse events during his life.
Regards,
Kai