I don't know if it was a bug or something else, but I just ran a quick Manifest mission as part of a Capitan Mercenary quest in the Shores of Plenty. The storm was nearby, but I never was fully engulfed within it.
I hit three floating barrel locations:
-First had three crates and a barrel with a note. I harpooned two of the crates, several barrels and then dove in to grab the last remaining crate.
-Second was a bottle with two or three crates and the key. I harpooned all onboard, and just to see if I found the key, I moved one crate on my ship.
-Third was the final location. The shipwreck was gone but the manifest remained floating on the water (old bug I believe). I picked it up and went straight to Sanctuary to sell.
When I arrived at Sanctuary I sold (at the merchant) the manifest first and upon returning to my ship all the "auto"-harpooned loot was gone. The crate I picked up was still there as well as the crate I moved on deck. I don't know when it all vanished.
Glad it was a short mission. I never saw another player and was only on for about 20 minutes.
