Hey John,
No, LimeLM doesn't deactivate your keys (randomly or without your knowledge). Have you enabled deactivating in your app (using the TurboActivate "Deactivate()" function)? Do you use the deactivation web API? Is one of the users on your account deactivating the activations?
If you email us product keys that show this behavior we can tell you whether the end-user deactivated the keys or someone on your end did it.