The net flux through the surface of the cube can be positive, negative or zero.  It is proportional to the number of field lines leaving the cube minus the number of field entering the cube.

net flux = constant*(# of field lines leaving - # of field lines entering).

Gauss' law tells us that the net electric flux through the surface of the cube is q_inside/ε₀.
The charge in this demo is q = ±1 nC. and there are 41 field lines either starting or ending on q.

When counting field lines we therefore know that the constant we need to use to find the electric flux is  (q_inside/ε₀)/41.

net flux = (q_inside/ε₀)*(# of field lines leaving - # of field lines entering)/41.