When the Earthquake shook the city of Gotham. All hell pretty much breaks loose. Gordon and his unit spray paint GCPD as way of taking back the city.
Now pf course it could be something totally different. There were many different symbols spray painted all over Gotham during this time period. Even Batman himself took part in spray painting the bat symbol in yellow along the walls. However, it's safe to go this in this direction rather than the speculation of the Levitt playing the Riddler leaving clues on the wall for Batman to solve.
My guess is, this is what Gordon is having Blake spray paint on the walls of Gotham as they take the city back from Bane and the other criminals.