The Eyepatch shouldn't be missable, it's just glitched so that it can be missed.
If you get the notes, memoirs, whatever the thing in the desert in the chest is before you talk to the sheep in the nearby camp, then he will disappear and you can't get the eyepatch. You have to talk to him before you do it, otherwise you're S.O.L.
That said, unless you haven't gotten the memoir or whatever it is, you will have to restart the game or load an earlier save in order to get the all items achievement. To make it easier, though, you can get the New Game+ DLC where you'll get to keep everything you currently have in your next playthrough. It'd be much easier since you start with level 99 characters, and shouldn't take nearly as long (you can skip the cutscenes, don't worry about any other achievements, and destroy everything in your path with ease).