I had this issue recently as well on the Ancient Cyclops in OOT. I scrambled for almost 7 minutes trying to loot it and re log to update the corpse. In the end, what i think was happening, was that the actual "deathspot" was at the surface of the water, but your request to loot is based on the graphical corpse location which sinks. So the corpse location and graphic weren't in sync.
Eventually I was able to find that sweet spot where I was close enough to the "corpse cube" and the "corpse graphic" to gain access.
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