This happened to me once when I placed a turret on the rounded surface of a water tank and it sank into the ground one block deep. So it never vanished and I got it back after removing the water tank and a block underneath.
Mmmh, I probably should make a bug report if I can duplicate this. Same goes for you, if you play vanilla and can replicate the issue (video helps too) make a bug report (in the bug report section, link is shown prominently above)