I've had all sorts of low tier structures and pillars decay after time, but have never lost a dino to it. Logging in every day I guess you just don't suspect the game to delete your tames as viciously as a random pillar.
And the only way to "prevent it" was to tame another damn rex to save the first one, which i did too late unaware it was already deleted! You can not just run, fly, wall climb with an enforcer, grapple etc your way into the underground forests cave. I tried one method almost EVERY night until I had enough time to waste taming a rex to get me down there.