Ok here is the logical thing that would have occured. If Amazo had copied Superman's (post crisis) powers then theoretically he would be able to absorb sunlight and use it for power like Superman does. Ok so he wanders space for 800 centuries and comes back to Earth. The whole time Superman had been sitting in the SUPER SUN. Amazo had already copied Superman's powers which are essentially the same except multiplied to ridiculous levels.
So there would be nothing else for him to copy from Superman Prime. He would have to spend the same amount of time inside the Super Sun. There would be no way that he could beat Superman Prime.
Granted Amazo was probably absorbing sunlight his entire trek through space but not all of it was yellow sunlight and it was not to the magnitude of Prime sitting in the Super Sun.
Prime would either destroy Amazo or turn him into a shiny new vacuum cleaner for Lois to clean the Fortress of Solitude with.