Tiano,
There is a Knowledge Base article, which I have linked below, which describes how to change your pulse train frequency on the fly.
How Do I Change The Frequency Output Of My Pulse Train On The Fly?
http://digital.ni.com/public.nsf/websearch/7B1B0427C39FE33086256CEE00752133?OpenDocument
However, since your pulse train is finite, and not continuous, you could just output your finite pulse train, reconfigure the counter for a new frequency, and output another finite train.
Also, the example you mentioned specifically refers to devices using the AM9513 chip. E-Series boards have the DAQ-STC chip, which is a custom ASIC designed by National Instruments. Examples written for the AM9513 are not compatible with the DAQ-STC, and vice versa.
Re
gards,
Justin Britten
Applications Engineer
National Instruments