I thought like "could have PP" is always what describes something that was able to be done but actually didn't.
Could can mean a hypothetical, but it is also the past form of can, which can refer to permission, possibility, or ability. Thus, "What could have changed you" is "what had the ability to change you". The full question means "what had the ability to change you in such a manner" or "to such an extent".
It is an expression of disbelief or surprise.
We can use 'what could have' to express surprise or near-disbelief about something that has happened. What could have damaged my car so much (it is squashed flat)?