Not-so-deadly Encounter
So as it turns out if El Tiburon drops his axe he'll do a knockout animation with his fists. To make him drop the axe throw a smoke bomb while in range to be instantly killed by him while there is an object in between you two to prevent the kill animation. El Tiburon will draw out his weapon and drop it. Getting near him will cause him to perform a high profile running knockout.
Now here's the big shock. Being knocked out doesn't desynch Edward! Instead it merely takes his health down nearly all the way. you will eventually desynch from losing sight of the captain.
Remove Swords
Getting knocked out will cause Edward to drop his dual swords, regardless if they're sheathed or unsheathed. If you get knocked out before the game autosaves from reaching the checkpoint "steal the captain key" when you reload the last checkpoint you'll start out without the swords. Too bad you'll regain them when you get out of the replay, although I suspect if you're going through the game the first time you won't get them back until you escape from the ships prison at the end of sequence 2.
As it happens some people have mysteriously lost their dual swords permanently (without re equiping them at shops of course).
http://www.gamefaqs.com/boards/705969-assassins-creed-iv-black-flag/7021...
So who knows if there is a way to permanently remove the swords.
Reversing the Knockout
To "regain consciousness" Edward has to experience a fall. It's not easy because even standing at the edge of a ledge he won't simply fall off when knocked out. It has to be done in a space too small for him fit on. The example in the video isn't that good since I desynch from being seen, but it gives you the point. I've managed to successfully do this without a desynch, but didn't get that recorded. Afterward Edward's health heals and everything is back to normal. You don't lose the swords in this case because the knockout animation wasn't completely finished when it got reversed.
El Tiburon Fighting Pirates
Interested in seeing if El Tiburon would perform one-hit kills on other characters, I hired a group of pirates. No such luck.