Hi Pedram,
1. The axis IsUsed property is a calculated property and is not immediately updated - you can force the property to update by calling the chart control document Calculate method:
nChartControl1.Document.Calculate();
2. Most likely the control document is left damaged by this operation because you removed custom axes, but obviously there are series that scale on them. To correct the problem you also need to loop through the series and turn off their display on axis property for each removed axis id.
Hope this helps - let us know if you meet any problems...