Lavos (Defeat Time)
Defeat Lavos's shell in 1999 A.D., and his shell is missing at the end of Black Omen confrontations in earlier eras. He's also the same strength each time you fight him. Also, if you confront Lavos at the Black Omen in any time period and lose, the 1999 A.D. destruction plays.
What era is Lavos defeated in, anyway? Is it 1999 A.D., or 12000 B.C. after going through the Black Omen?
To the same-strength question, Thought: Generally, once creatures reach adulthood, their strength and size does not increase dramatically. A black bear at the age of 7 will be about as fearsome as a black bear at the age of 10. While there will be changes, those are comparatively small when put next to the changes between child and adult. Lavos has been feeding on the planet since 65,000,000 BC and "growing stronger," but it is entirely possible that all such energies when into reproduction and assimilation, not towards increasing its raw strength. Furthermore, the earliest we can fight Lavos is 12,000 BC. That gives him 64,988,000 years to develop and grow strong, whatever that means. In contrast, the 13,999 year difference between the earliest and the latest one can face Lavos seems negligible.
To the time of defeat question, the Compendium holds that he was defeated in 1999 A.D. This jives with existing phenomena and also enables the Armageddon-Branch theory in Salt for the Dead Sea. To enable this, there's another theory below:
When Zeal taps into the power of Lavos, calling upon his awakening, we see a blue circle expand beneath the Omen. This is not Lavos awakening; this is a gate opening. Upon her defeat a gate opens up beneath the Omen and transports the party to 1999 AD and Lavos's awakening. The disintegration of the Omen is the physical transformation of the Omen into a gate, to fulfill Zeal's wishes of Lavos facing our heroes and destroying them. Because the Omen is sacrificed to make the gate, it no longer exists in 1999 or any time after it makes the transformation into a gate to 1999 A.D. The party can only fight Lavos in this time period.