In my haste to reprogram the DataFlash card on Friday, I think I may have accidentally erased the Boot ROM. I know now that I forgot to select the DataFlash card as the source to enable and write to, and blindly erased/wrote to the default setting in SAM-BA. Now when I power on the board, regardless of what I do, I do not see any output on the serial console. Is there any way to recover this?

Well you'll have a hard time erasing the Boot ROM.

What's more likely happening is that the vectors in the NAND or Data Flash are being executed.

General recovery methods for SAM9xxx devices are pushing the button the bootstrap code is looking for to erase the flash, pulling the jumper or connection for the flash chip's select pin, breaking errant code with a JTAG pod and erasing the flash device(s), or delivering bootstrap code in a device that's earlier in the Boot ROM's probing sequence.