I do flatten quite frequently and to answer your question...yes I flattened after I did the screened copies. I also would have flattened after the color fills, after the unsharp mask, after the sharpen and after the blur steps. In my mind that's all part of "fixing" the base image so I want to end up with a single "good" base image. When I get to the point where I'm adding textures and playing around with those settings I would generally have a saved unflattened file (PSD for photoshop or XCF for gimp) so I can mess around with the different layers.