I looked at the project.. and it appears you have only animated a small portion. Each item on there needs to have it's animation applied along the timeline with it's own "range" that does not interfere with the other. For example, don't overlap the handle animation with the clips, and the top handle with the latches. Do each part in pairs or parts separate for their paired or separate animations, with their own range to be collected later.
I did a test with the items in pairs and it took it out to a bit over 900 frames, but each pair is animated and separate in range on the time line, so they can be identified for collection at the end of the transforms stage.
I then merged them to the base box, and all the ranges are clearly easy to define, due to clips using range 400-500, and side handles using range 600-700 as two examples. The sequences are independent of each other.
I then collect on what I see animated during those ranges, and then give it a proper name for the collection, "side handles up" or "side handles down", side clips open/close, or whatever you want to call them.
Regardless of the part they are sitting on, (Bottom/Lid) the animation will be independent once given a name. I just did all the animation transforms primarily with the lid closed, but it won't matter after the collection and named commands are given. They are still independent sequences if collected as separate sequences.
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