Reconfigurate the FPGA image from the Nios II software

Naturally, you need to drive the configuration pin from fpga if you want nios to a have a go into the unknown afterlife.

Are you sure your new nios will tick again, consider having a default image that is never touched(sacred image) just in case of emergency especially with remote applications.

edit:

Make sure that the user at their premises can reconfigure the fpga e.g. from board jumpers in case the new remote didn't work otherwise you have to fly there with your full gear unless a default image is loaded automatically.