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Well my interpretations are just my own speculations from viewing the movie once.
What I saw was that everytime the ELS interacted with a QBW user, it was shown that the waves were coming from the ELS and the QBW user senses it and gets a headache.
What makes it more likely that the ELS has QBW was because Setsuna said himself that he wants to establish a connection with them using QBW inside the quantum realm, which was his intention all the way till the end.
The only problem Setsuna faced other than the headaches was the lack of power to generate the amount of GN Particles he needs to establish a strong enough connection.
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