The entropy of the system in a canonical ensemble is given by the Gibbs entropy formula. This formula depends on the choice of microstates. For example, if I model $\mathbb R^3$ by a lattice and do the simplifying assumption that each molecule is on a grid point, then the entropy is dependent on the density of the lattice.
On the other hand, change in entropy is also defined by $$dS=\frac{dQ_{rev}}{T}.$$ This seems independent of the choice of microstates.
So for example, suppose that a gas is in some box and then it all flows out of that box. The entropy goes from $S$ to zero. When we use the Gibbs entropy formula, then the difference between initial and final entropy in the box depends on the choice of microstates. But when we use the other equation, it only depends on the number of heat that flowed out.