Did the surviving Jedi ever found out that it was the chips that made the clones betray them? Or they kept thinking that the clones willingly betrayed them?

padawanlost:

I’m not sure. Some of them,
the ones who knew about the chips and survived Order 66 probably made the connection.
The whole chip story is complicated because that arc belongs to season 6 of TCW
and when season 6 was aired SW already belonged to Disney and Disney had put a
halt on the EU stuff. That arc and its consequences was never explored in
George’s SW.

People complain
that we never saw Anakin’s reaction to Fives death or that chips were “forgotten”
but they forget the reason we never got any follow up on that arc is because
Disney pulled the plug and we never got any EU stuff to fill the gaps. The only thing that is kind of set around the Order 66 time is the Ahsoka book (Disney’s canon). She seems to
understand the chip is the reason the clones turned on her but I’m assuming Rex
told her about Fives because she was not there for any of that arc.

“[Ahsoka] thought about all the clone troopers
she had ever served with. They had been so quick to accept her, even when she
first became Anakin’s Padawan. Sure, part of that was their genetic code, but
that only went so far. They respected her. They listened to her. They taught
her everything they knew. And when she made mistakes, when she got some of them
killed, they forgave her, and they stood beside her again when it was time to
return to battle. The Jedi were gone, but what happened to the clones was
almost worse. Their identities, their
free will, removed with a simple voice command and the activation of a chip. If
she hadn’t seen it for herself, she wouldn’t have believed it was possible.” Ahsoka,
E.K Johnston

to keep it simple:

• Disney’s canon: some of them did.
• George’s canon: we don’t know for sure who knew what.