It just goes to show you they do have feelings...jumbled, but yes, they are feeling pain too.
What does your gut tell you to do?
I think the occasional compliment is a good thing. Everyone deserves as much and esp. from our spouses. Every time my H tells me I look good, I've done a great job losing the baby weight, etc. it means a lot.
I don't know if the email or letter is the way to go. But I think when the time is right, and it might be an email, you should let her know that while you don't understand exactly what she's going through, you are going to let her, you understand this process has to happen and she has to live it, make her mistakes, live her accomplishments and own them all herself. Just like you have to do the same thing.