Minecraft 1.9.2: Ender chest disappearing in End after death
Solution 1:
Every time you enter The End the obsidian platform is regenerated and three high space above it is cleared from any blocks. If you placed the chest directly on the obsidian platform, it would be deleted.
If the disappearing chest is somewhere else in The End you might be experiencing a very weird and oddly specific glitch, which is unlikely. The dragon doesn't move while you are not in The End, so it won't be destroying the chest without you being able to witness it.