I don't think Yorha literally repeats. The war does, and many machines/androids who have fought many times are rebuilt/repurposed, but I think this is the one and only war where Yorha was a factor.
There's only one generation of Yorha androids besides the prototype run that A2 is the last member of. If the Yorha cycle literally repeated, surely 1. the non-Yorha androids on Earth would instantly know what was up and 2. wouldn't Yorha spec androids be all over the place/not a "new" design? If Yorha and the machine network were the only characters in play, I think the literal repeating test/cycle would make more sense, but there's a whole world of androids out there who would surely notice that Yorha kept getting built up and torn down. The logic virus only targets Yorha if I remember correctly, so it's not like it's an android-wide apocalyptic event.
When the Pods refer to the possibility that "everything could happen the same way again," I think they're referring to the cycle of violence and war that has happened so many times previously, not a literal repeating of the same cycle. I could be wrong though, but right now I'm leaning more towards the cycle being figurative more than literal.
EDIT - I would submit that there is evidence for this interpretation in the fact that their recorded date continues to tick up from the original Nier's - time is still marching forward and everyone is aware of it.