I've been merging my libraries into a single big one and I had the same issue happen with some of my images turning green. I spent a lot of time trying to figure it out and finally what did it was to re-generate all previews. Took a while but it worked. I wrote a blog post with the details here: http://bit.ly/eD0yAL
I ended up also generating thumbnails even though it worked by just doing the previews. Hope that helps.