The CPU time increases when you request that checks be made for flooding and drying. For an estimate please see CPU Time.
In order to avoid drying and flooding following rapidly after each other (which will lead to instabilities in the computations) a point is not dried out if the water depths at the four grid points immediately below, above, to the right and to the left all are larger than the flooding depth. However, if the depth at the point in question is nearly zero, it is always dried out.
A point is flooded if the water level at one of the four grid points immediately below, above, to the right or to the left is more than the value you have specified as the minimum flooding depth.
If you have instabilities in your model, you might be able to avoid them by first of all checking for flooding and drying after each time step. If the problems persist, you can increase the drying and flooding depths and, in particular, the difference between the two.
Continuity is preserved during the flooding and drying process as the water depths at the points which are dried out are saved and then reused when the point becomes flooded again. However, in cases of excessive flooding and drying, e.g. during rainfall on otherwise dry land, the model may resort to numerical water level correction in order to stabilize the model. This may give reason to inconsistency in the water balance. For more details, and how to reduce inconsistency, please see the section on Flooding and Drying in the MIKE 21 HD Scientific Background.