Thanks for the feedback!
I have considered the concept of "projects" before but felt it was adding a layer of complexity that wasn't really required.
I very much like the idea of being able to launch the program back exactly where you left it. There are some pieces already in there that should make this not too complicated. In particular the crash recovery mechanism is able to restore the state of the video + analysis after a crash even if it wasn't explicitly saved. This works through a special field in the KVA file that references the video it was created on.
From reading your post I feel that the KVA file with the video reference is already matching the concept of "project" that you describe? A key missing feature is the ability to open a KVA file and automatically load the video it references. Also it would need to push back the state of zoom/scale, mirror, magnifier, working zone and current position of playhead.
"Load key image data" is important in itself to be able to load several KVA files onto a single video. This is useful for comparison purposes for example, or if you have a standard KVA with template lines or other reference material.
Regarding opening a video in the active window, I haven't received a lot of feedback about this. You can replace the first video by drag & drop from the explorer. The algorithm tries to make things work intuitively based on the state of the screens, especially for the case where there is an empty screen or if the single screen is a capture one. But yeah, when both screens are filled, the "open video" menu could take the active one into account. Although I'm not sure if replacing the active one is the most intuitive, you could argue that the user is working on it so it might be better to replace the other one. I don't feel the active screen is a really safe hint to rely on here. I agree that the current way, replacing the second screen, is not perfect.
The file explorer should switch to the directory containing the last opened video so if the user really wants to control where to open the next file when the two screens are already used, the drag & drop method should be the easiest and safest way.