I had an issue similar to this where aseprite could not guess related files, so what I did was I just dragged them all in as individual files, then wrote a script jest merge all tabs Aseprite Scripts Collection - #40 by jest to merge them together into 1 file.
Really the solution is aseprite just shouldn’t guess at all, by dragging in a bunch of files, you the user are already acknowledging they’re related in some way so it should just prompt and ask you how they’re related or if they’re not: Always prompt user to import as animation or as layers like other paint applications · Issue #2648 · aseprite/aseprite · GitHub . I was looking into implementing this but I think it would break a lot of the scripting API among other things.