Except Waterloo occurred after Nappy had already been exiled, and returned. The losses in Russia were years ago, and there were many cohorts (each annual class of men is considered a cohort) since that happened that were able to replenish the French Army. About half the Grande Armee were not French. Spanish and Portuguese soldiers were particularly prone to desertion.
Wellington had already fought the French in Spain.
The Russian campaign was in 1812 and 1813; he was barely able to extricate himself in the east, and returned to France outnumbered 3:1. He was forced out of power in 1814 (one year, not years later), and returned from his first exile in 1815. In the space of three months the allies brought their armies back into theater, Napoleon threw together one last army, and went on the attack against a numerically superior enemy that was already dug in. He wasn’t able to dislodge them before the Prussian army arrived on his flank.