Flint initially had 12 sheep.
- At night, 2 ran away, leaving him with \( 12 - 2 = 10 \) sheep.
- In the morning, 1 of those 10 was eaten, leaving him with \( 10 - 1 = 9 \) sheep.
- The next day, the 2 sheep that ran away came back, so he had \( 9 + 2 = 11 \) sheep.
Thus, Flint has 11 sheep left.