MAYBE SPOILER(ish)?
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A lot of things played a part in him finding out. Neuta brought up the madeleine he had received from his neighbour. He also said that he modelled his character's appearance after his neighbour. Afterwards, Ji9star heard the same sounds both outside his flat and during their call. He also knew that Neuta was sick and surprise, his neighbor was sick at the same time. He connected the dots and found out.
When Jigu and Yeowoon were out in the rain Jigu's mom made him give Yeowoon Madeleines. Yeowoon then later sent the picture to Jigu (jistar) online and thats when Jigu started suspecting Yeowoon to be Neuta
When Yeowoon was at Jigu's place he got a message the same time that Jigu sent a message to Neuta. Jigu asked him if the friend who messaged him was someone he met through a game and Yeowoon confirmed it.
I think that was the time Jigu also confimed that Yeowoon = Neuta
Is it just me? I'm still wondering how he find out about neuta's identity