Question about Flashbacks - SPOILERS

I actually have no answers to these questions as I was wondering very similar things to yourself.

The significance of Traudes past, of her relationship with the blonde lady and how this ultimately related to her interest in Jenny is slightly blurry to me.

All i have are speculations...

What i got from the movie is that the building where the women are held prisoner is the building where the older woman worked as a nurse in the war and where her lover was killed. I thought she kept working there because she wanted to be near her in some way.

As for what was in the file, good question. Perhaps that there were whispers during the war that she was a lesbian. (don;t forget that people were killed for being gay) And that she still hadn't told anybody about her true self.

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I think the interpretation that Traude stayed in the prison in order to remain close to her lover is correct. In addition, I think Traude felt guilty because she had been spared back then, and imposed her own judgement upon herself: she gave up her very promising musical career (as one of Wilhelm Furtwängler's best students!) and stayed in that prison for the rest of her life.

I think Traude and Hannah met at work - I don't think Traude took the job to be near Hannah. Don't they both wear the same nurse uniform in the first flashback? Hannah was later discovered to be a communist, and since she was already working in a prison, it was convenient to imprison her in the very same place.

I don't think their relationship (or their homosexuality in general) was the main issue in the trial, or they would have found a pretext to convict Traude as well. I think the officer that later interrogates Traude knew (or had some suspicion) about their relationship - that's why he suggested to Traude to deny it. (I think he wanted to help Traude - but there was no way anyone could possibly have helped Hannah.)

As for the file, this remains the main question. We hear Traude reading some parts of the file aloud, and all it seems to say is that she was interrogated regarding Hannah, and that she claimed not to have known her very well.
I agree with all of you, it is a complete mystery to me how Jenny's father could deduce the whole story from these few pieces of information, or, and that's even more of a mystery, why he started to look for it in the first place.
I'd be happy if someone could clear that up one day!

On a related note, I also have some questions regarding a specific flashback scene - I posted them here:
http://www.imdb.com/title/tt0461694/board/thread/160200633
Please have a look, I'm curious to read your opinion.