The easiest way to work around the 250 variable limit is to export data by groups of the same element type (i.e. routerSwitch). No matter the number of elements in the group, the limit will not be exceeded. OneClick for eHealth can list elements by element type, so it is a simple matter to create groups based on types.
If that is not workable, the next best thing is to export smaller groups of elements. Usually, a few thousand elements will stay under the 250 variable limit.