@Hylie Pistof : I kept the Flushdeck from the main quest. It's supposed to be seized (and thus "disappear") once you get to Port Royale, as you've experienced. The key is to swap the Flushdeck with another ship. However, it won't let you (the "Ship" menu is grayed out) even when in peaceful waters on the way to Port Royale. I didn't know this last part until retrying it just now. In my game, when I attempted to leave Speightstown, I was fired upon in port, and my Raa class had been replaced with the Flushdeck while my Aurora class was still with me. I was going to flee, but I saw a class 2 Centurion which was irresistible, so I charged it to the point of boarding it. I swapped the Flushdeck with the Centurion class, and this turned out to be key. When I arrived at Port Royale, they took my Centurion class, but left the Flushdeck alone. So I figured they'll simply seize whatever ship is in the first ship slot, since it's assumed to be the Flushdeck.
Luckily, I had saved it just before Port Royale. Interestingly, there's something about that capture/swap I did that reenables the "Ship" menu, thus allowing me to swap the Centurion with the Aurora, which was now in the first slot (Flushdeck still in the second). So what did Silehard seize? The Aurora, of course. They replaced it with the Raa class that "disappeared" at Speightstown. I was pleased. Of course, recall that my game or computer may be buggy. However, I just now reproduced this same result, but on purpose this time. Note that I've been sailing for 16 in-game months without issues with my ships or ship slots since keeping the Flushdeck.
Long story short: Capture a ship before Port Royale. Swap. Ensure you have a ship in slot 1 that you don't care about losing. Go to Port Royale. Slot 1 ship seized. Flushdeck is yours. Celebratory double rum rations!
Long story unnecessarily longer: I wanted to note that I also just tried a different method. Instead of capturing a ship at all, I just fled Speightstown to open sea and could not access the "Ship" menu, as previously noted. However, I tried to trick it. I went to my other ship's deck and the "Ship" menu became available. I was able to swap ships. But as soon as I switch to the world map, the game crashes on me. Exact same point every time. Just letting you know I tried this method and it doesn't work... at least not for me. Maybe it can work for you. The capture/swap method above does, though, and it's easy, so no worries.