If you run out of Cities, Towns, Explorers, or Blight in the supply, you should use Energy Markers as “1 more / 3 more of this piece” markers to represent additional pieces as needed. The number of Invaders is not limited by the supply of pieces.

This is stated on page 15:

The number of Invaders is not limited by the supply of pieces; in the unlikely case that you run out, use Energy Markers as “1 more / 3 more of this piece” markers.

For Blight, if you run out of Blight on the Blight Card, you must follow the instructions on the Blight Card—either “lose” or “flip the card over and do what it says on the reverse.” If all Blight on the Blighted side runs out, the players lose.

Source: page 15.

Source: Core Rulebook (pp. 10, 11, 15, 30, 9)