She's actually made progress. But, today... .
I don't think BPD can ever be "cured". Therapy should reduce the number of episodes, or reduce their strength, but it can never make them go away. So if she's made progress, but still slips - that's to be expected.
I've gotten the silent treatment for 10 days and nothing I say can break her out of her funk. I've tried to acknowledge her feelings. I've tried to explain context and what I was thinking at the time and that I wasn't thinking the way she's worried about. I've tried to explain that the way I write something to myself is not the same as she would write something. It doesn't make a difference. She says she can't stay with someone that thinks about her in the way she worries I do. Ugh.
What do I do now?
If you've known about BPD for a few years I presume you know that LOGIC doesn't help her. It sounds like you tried Validating her feelings - which is good. Any logic (explaining) after that was pointless. I presume part of your validation was an apology (not for doing something wrong, but for doing something that upset her).
She's feeling hurt/angry/whatever. Some is real pain, but i think a lot of it is "I'm a poor victim". Perhaps even she's afraid of being happy because she may lose you again. It doesn't really matter. I suggest you leave her alone. Go about your life. Have fun. Be happy. Invite her to have fun and be happy with you. She'll call you insensitive because you're not wallowing in sorrow with her. You can say broken record: "I know things I've done in the past have made you upset. I want to move forward and have a happy marriage with you".
She is worried that you may leave again, she's probably trying to find evidence so she doesn't have to trust you again. Be strong, be sure, be confident. I think the stronger a leader you are, the more she is inclined to follow. The more she is inclined to trust you.