Server transfer = lost shoulder pet - work around.

[Captain Jack Shadow 488]

So you have your shoulder pet on your shoulder, and you transfer from one grid to another, and notice your shoulder pet is gone...but is it?  Hint...look at the buff at the bottom right.  See if you still have the buff.  If you do, the shoulder pet is still on your shoulder.  However, I don't think this means you can just go about your business.  I have lost parrots, monkeys, and other shoulder pets this way.  However tonight, I wanted to see if the crow was somewhere on the ship.  It was not.  I then noticed that an image of it was flashing around the ship, and it appeared to be sitting on an invisible shoulder.  I then noticed that I still had the brain buff.  So I logged out, and logged back in.  The crow was now standing on the deck behind me.  I don't know if this situation was the same as all the other shoulder pets I lost, but I suspect it was.  The thing is, those never came back, so if it was the same situation, then logging out on the spot, and logging right back in is the fix to keep them from permanently disappearing.

[Ducimus 35]

mine usually starts to fly around in the distance.. when u try to get closer it just flyes further out xD 

[Captain Jack Shadow 488]

2 hours ago, Ducimus said:

mine usually starts to fly around in the distance.. when u try to get closer it just flyes further out xD 

That is what I was seeing, in a way.  I think you had the same problem.  Next time, just stop the ship immediately, and after making sure it is safe to do so, log out, and log back in.  You will likely find that the shoulder pet is now standing on the deck behind you.

[SIEGEGUN 57]

I have never lost a shoulder pet while it was on my shoulder, but lost 2 monkeys, npc, and at least 3 or 4 bears off my ship. I am replying because of your "invisible" comment. When I lost the bears, it was when loading them on my ship. Two just disappeared, couldn't find them anywhere, whistling did not help. They were just gone. Hanging out with Elvis and the rest of the lost tames in this game I am assuming. The third time it happened though the sun was low in the horizon and when I looked at where the bear should be I saw the shadow of my bear on the deck. No bear, just his shadow. I ran around it through it etc trying to make something happen. Nothing. So I whistled the bear as a last resort and he magically reappeared on my deck. 

Just found it interesting the "invisibility" issue was there for both occasions, yours and mine. Oh I did try logging in and out for the first two bears, nothing.