Extinction of Factions

These factions were destroyed during the Seven Hour War. However, except for Aperture Science, Buy n Large, and Area 57, they are not destroyed.

2139: Omnicorp
Following the destruction of City 17 in Seven Hour War, Omnicorp was indeed destroyed from history, although various other Combine units that it sent back in time to kill humans remained in existence, following orders that Omnicorp no longer existed.

2187 A.D.: Combine
However, in City 17: A FNwES Story during the 145 years later, Dog destroyed the master pillar before Combine Overworld could fully emerge from the portal, and the planet seemingly collapsed as it fell back through the portal.