Thank you all for your help. With your help and little guidance from Altera support I was able to solve my problem. It's not a perfect solution but it is good enough for a little while.
I downloaded the Quartus Programmer, I connected the bit-blaster to the JTAG port and after a little debugging of the JTAG chain I was able to talk again to the EPC16. I "Examined" the data on board which saved it to my hard drive. I then got another board that did not work and used the "Program/Configure" option to write it to the EPC16. We powered the board on and the board in question worked for the first time in it's lifetime.
Thank you so much! I can not express what a relief I feel after getting this all working correctly.