Nolisan,
I think I would have felt the same way if my T had said that to me. In fact, the other day when I was trying to get an appt. with mine, she didn't have the time I usually meet with her, and I felt myself responding with anger (inside) like, "Why doesn't she have time for me anymore?" This definitely comes from my FOO: absent father, working mother, etc., and I suppose it's really normal to transfer all that to the T.
I think this remark by your therapist that triggered the feeling of abandonment is a good opportunity to go there with her, as it sounds like she has been helpful and you trust her.
I totally relate about feeling like damaged goods and not being capable of having healthy relationships! I guess I just don't believe it anymore. So many other things haven't been true either
You are definitely not alone, nolisan. Keep us posted on how you are doing.