Before answering your question, let me just say what I mean by the entropy of an isolated Hamiltonian system. You first choose your favorite set of macrovariables, those that will be used to define the relevant notion of macrostate. You then partition phase space into subsets according to the values taken by these variables (say, up to some given precision). Then, to a given microstate $\omega$, you associate an entropy given by the logarithm of the measure of the subset it belongs to.
For more on this, see, for instance, the paper
Macroscopic laws, microscopic dynamics, time's arrow and Boltzmann's entropy, J. Lebowitz, Physica A 194 (1993) 1-27, or this more recent one by the same author.
Now, let us turn to your question.
You are confusing micro- and macrostates. Suppose that the gas starts at time $0$ with all particles in the left half of the box. This corresponds to a nonequilibrium macrostate (which can be obtained by compressing the gas and inserting a removable wall to keep it there; and removing the wall at time $0$). Let us call $A$ the corresponding subset of phase space.
At positive times, the system evolves, the molecules distributing themselves in the whole box in an essentially homogeneous way, with overwhelming probability. If $A_t$ denotes the image of $A$ at time $t$, then when $t\gg 1$, the vast majority of points in $A_t$ belong to the equilibrium macrostate $B$.
Of course, the Liouville measure of $A_t$ is equal to the Liouville measure of the original set $A$. However, the measure of the set $A_t$ is ridiculously small compared to the measure of the equilibrium macrostate $B$: the points in $A_t$ comprise only a minuscule fraction of the equilibrium macrostate $B$, namely those points corresponding to microstates in which all particles were in the left half of the box at time $0$.
So, if you were to start from any point in $A_t$ and reverse all velocities, the system would return to its initial state at time $0$, displaying a decrease of entropy along the trajectory. However, if you sample a random point in the equilibrium macrostate $B$, then it will almost certainly not belong to $A_t$ and would remain at equilibrium.
So, such Hamiltonian systems are reversible in the mechanical sense: upon reversing velocities, the system follows the same trajectory in reverse. However, it is not reversible in the thermodynamic sense: taking a generic point in the equilibrium macrostate will not lead to the same evolution as selecting a point in the extremely pathological subset $A_t$.
Above, I have assumed that one has waited for the system to reach equilibrium, but the same discussion also applies if you look at what happens at a time $t$ before equilibrium has been reached: the system will find itself in another macrostate, with Liouville measure much larger than that of $A_t$. Sampling a generic point in this macrostate and reversing its velocities will lead to trajectories along which entropy increases (until equilibrium is reached), even though entropy would decrease if you do that for points belonging to $A_t$.