First, be careful when upgrading the EPCS dynamically because there is no multi-region available and then you can not have User and Factory like structure. Then, if the transfert fails, your EPCS might be corrupted and your board will be dead. http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/ph34r.gif
I will advice you to use a local memory in which you will transfert the contents (external SRAM or SDRAM). Once the transfer into the local memory is completed, do erase and rewrite the entire EPCS. Be sure that no power down will occur. Again, you could get a piece of wood
http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/smile.gif .
Otherwise, HAL provides you with sufficient driver to erase and write into the EPCS. EPCS is just a serial Flash. You should be able to implement your own mecanism upgrading the EPCS.
Maga