Is the transition from NPP South to Generators also missing? There have been a couple of other reports of transitions going missing recently.
Please send your save game, with a brief explanation of the problem, to Aleks ( adoler(at)gmail.com ). Hopefully he will be able to figure out what has gone wrong and send you a fix.
In the meantime, you can use the 'teleport' cheat menu [ESC]+[F2] to enter Generators. gencamp takes you to the stalker camp, or gennorth drops you where you first arrived with Ghost.
If you no longer have the paths out of Generators either, you can use Strelok's teleporter to AW, or again use [ESC]+[F2] to another map.
General (but important) caveat: Do not use the teleport menu unless you have no alternative. Entering a new map before you are supposed to can make the game think you are at a different point in the story; and skipping a correct map entry point can mean missing an important event.