Two glitches:
1) If you run a clock to execute /setworldspawn around an entity, teleport the entity into ungenerated chunks, then teleport to the entity, it will delete said entity.
2) Previous to 15w39a/b/c, teleporting away and back to the entity would have the same effect.

To Replicate:
1) Create a new superflat creative world.
2) Give yourself a repeating command block and place it down.
3) Put in '/execute @e[type=ArmorStand] ~ ~ ~ /setworldspawn ~ ~ ~' the command block, and apply any kind of redstone.
4) Summon an ArmorStand at your feet.
5) Run in chat '/tp @e[type=ArmorStand] ~2000 ~ ~', followed by '/tp ~2000 ~ ~'.
6) Armorstand is nowhere to be found.

The superflat world is just to guarantee you'll be on the ground. This still happens in default world type too. Even running an /execute command doesn't work. I hope you can get this solved, and I thank you for your time.