Seems there wasn't much of an appreciation for items of historic significance in those days. Although data is sketchy, HMS Resolution used in Cook's second and third voyages of discovery apparently suffered a similar ignominious fate (from Wikipedia)

Her fate, by some cruel twist of historical irony, is as incredible as Endeavour's – she [Resolution] was sold to the French, rechristened La Liberte, and transformed into a whaler, then ended her days rotting in Newport Harbor. She settled to the bottom just a mile from Endeavour

And yet items of monarchical conspicuous consumption like the crown jewels are afforded meticulous preservation resources. /s