Caveat Emptor

Forcing the PCs to part with their loot always is iffy - unless the game you play has a specific mechanic for blowing your money (like Conan: Adventures in an age undreamed of), getting players to part with their items is always tricky.

But there's two ways out of your situation:

Confessing you messed up

Talk to your players. Tell them that you messed up by having the NPC run and that they were not supposed to have that much money now. Ask them if they are ok to retcon the bounty down by the amount of the debt that the ship secured.

The debt doesn't go away.

The NPC is gone, but the boat still is one of his possessions. The town thus repossesses the boat as originally planned to cover the debt.

To get off the island, the PCs would need to buy the boat and hire a crew, which costs them a lot of money. Sure, they will now own a boat, but they can't lug that to dungeneering, and they can only sell it for a fraction of its worth in a different place - or they need to pay to keep the crew if they want to keep it.

Caveat Emptor

Forcing the PCs to part with their loot always is iffy - unless the game you play has a specific mechanic for blowing your money (like Conan: Adventures in an age undreamed of), getting players to part with their items is always tricky.

But there's two ways out of your situation:

Table Solution: Confessing you messed up

Talk to your players. Tell them that you messed up by having the NPC run and that they were not supposed to have that much money now. Ask them if they are ok to retcon the bounty down by the amount of the debt that the ship secured.

This works great if you know your players, and I used it a couple of times.

IC solution: No payment to the debtor means the debt doesn't go away.

The NPC is gone, but the boat still is one of his possessions and secured the debt. The town thus repossesses the boat as originally planned to cover the debt. Do note, that a sailing ship is worth at least 5 digits!

To get off the island, the PCs would need to buy the boat and hire a crew or pay for passage. This will cost them a lot of money, and with the price of ships, the 1800 gp they have now is not enough to pay for the boat in full. As the town has the only operator of a ship, they can dictate prices for passage.

If the party decides to try and buy the boat, note that they can't lug that to dungeneering, and they can only sell it for a fraction (half or less) of its worth in a different place. Also, they'd need to pay the crew wages to keep it running if they don't want to sell it.