No, game tracks what your active pirate got during the plunder run while on deck. You must be on deck of the ship to claim it when the ship finally ports. If you are AFK while on deck, game does not count any plunder taken by sunken ships. If you end up in the hull after leaving a flagship and that flagship drops loot, that won't count for your pirate. If you must teleport off the ship to buy more cannon ammo, game will resume tracking your share of the plunder as soon as your pirate teleports back and lands on deck.
POTCO is aware of certain flagship issues.
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