The above says something is seriously wrong. I suspect you are going to need to flash the system again, perhaps after cloning if there is something valuable on the AGX, but I am wondering how the package system ever made it to that state. Is there anything unusual about this Jetson?
because I want to install software for systems that require amd64. Now, I want to know whether the steps of reflashing system is as same as the steps of flashing system for the first time.
Did you run that on the Jetson? If so, then it will only mess up your system. The only legitimate use of the wrong architecture (which a Jetson has no ability to use) is if you are cross compiling from Jetson to host PC, or else going to run inside of an emulator for the amd64 architecture.