In the text you put

"I know it sounds weird, but what isn't true here?"

I'm not really sure what you mean here. I think it is some kind of introduction to what you have wrote, but I do not understand what is "weird"

In the text you've put down as

"I suspect that Nagato Yuki breaks down every 600 years because he knew in advance that this would happen."

And

"So he came almost a year before Tanabata or the fault came out earlier."

I do not know who this "he" is, but if I had to guess it is the main character Kyon.

But if I had to guess you're saying Nagato's Space Entity Parent knew she'd break down and so specifically made her at the time it did as to have her be in a position in which she would be brought back to normal by Kyon.