Does "you were ever my best friend" mean "you were friends in the past, but not now"? What does "ever" mean here?
Yes. You are correct that she is referring to the fact that they were friends and now aren't. "Ever" here means at any time or at any point. So she's saying she's sorry that they were best friends at any point. Ex: Nothing ever seems to upset her. Ex: He doesn't ever eat his vegetables.
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