Second Wave says, at the end of the game:

If the Blight Card is on the Blighted side: Return it to “Healthy”. Leave 2 Blight per player (plus 1) on it, and set the rest here. If it flips to Blighted ignore the amount of Blight printed on the Blighted side and instead use the Blight sitting here from the first game. (This will often be less than the printed amount, because some Blight has been left on the island.)

During gameplay, you can see on the scenario button the number of blight that will be added when the Blight card flips. In the example below, it's 4 Blight.