Did you place a workbench next to it to prevent the mats from despawning after it might have been destroyed? The loot will otherwise disappear after a certain time, so just asking. Aside from the usual damage through anything it might have come in touch with, I wouldn't know any other way it might have gone missing.
ofc you could switch back to the karve but would that help if it happens again? I mean yes, less/other mats to rebuild if needed. But the longboat is still safer (double the health of karve acc. to wiki), faster and has way more storage. Anyway, hope you find out what happened and can solve it somehow.