Arrows will disappear 1 minute later when using:

/data merge entity @e[type=minecraft:arrow,limit=1,sort=nearest] {life:10}

(on a fast clock and the same command but with life 11)
but still be in the game so you can still teleport to it or pick it up and relogging makes it reappear.

It is shot into a barrier block though the arrow will still disappear on other surfaces

Edit 14/5/17: Still not fixed, a light blue potion swirl particle effect will appear around arrows when the command is used.