In Constraint Programming, are there any models that take into account the number of variable changes?
It sounds like you want a cost-sensitive (cost-aware, budgeted) optimization technique. Minimizing two values (e.g. the solution of your objective and the cost of operations on $x$ and $y$) is a multicriteria optimization problem, and those tend to be very hard to solve. A common approach is to specify a budget for the maximum allowable costs and then minimize the objective function with respect to $costs(x,y) \le Budget$. This formulation tends to fit nicely into existing frameworks as an additional constraint. Of course, specifying the cost function and the allowable budget in such a way that you get meaningful solutions can be difficult - this will depend on the specific problem you are trying to solve.