Try something like this:
for (int i = 1; i < some_number; i++)
{
Control myControl = FindControl("CheckBox" + i.ToString());
if(myControl != null && myControl.GetType() == typeof(CheckBox))
{
((CheckBox)myControl).ID = "chckbx_" + i.ToString();
((CheckBox)myControl).CssClass = "newClass";
}
}