All loot tokens you accumulate are public information. If an ability requires a loot token to be discarded during the voyage, the token is put back in the bag; otherwise, tokens remain in your supply.
Loot abilities are described on the board (and on loot tiles for uncharted mode). Loot tokens with dusk abilities only trigger when they’re first gained, not on future dusk phases or if they’re passed from one player to another due to a character’s ability. Other loot tokens have abilities that trigger at night. Anchor abilities trigger at the end of the voyage.
Unless otherwise stated by a character or loot ability (e.g., the stormy side of the map tile), all loot tokens are put back in the bag at the end of each voyage.