Did you have the Storyboard docker opened? Also I assume that when you lost the Timeline docker, you got it back later? When you say you had only one layer, I assume that it was only one layer in the Layers docker, not the Timeline docker? Do you still have the file from three hours before the incident (if I understood correctly, you saved it)?
I did not have the storyboard docker opened. I didn’t lose the timeline, I just got it out of its place, like I was able to move it around everywhere, so I just put it back in the bottom part where it was supposed to be. Yeah, I still have that file, I continued working with it so it is further modified, but yeah, I’m using the same file (and I created a back-up too). Also, could it be memory saturation? I have 54GB free in my computer, but sometimes I have ten less because I’m watching YouTube at the same time, and sometimes the program gets a bit slow. When I used SAI2, sometimes the program lagged for a few seconds and then returned to normal. Could it be that saturation caused the bug? I have a kinda decent computer that can run some complex games, so it isn’t that bad. Maybe you can check how Krita behaves when saturated? That’s just my theory… I’ve used other programs like Clip Studio and it’s the first time it happens.