Welcome to the forum!
Before you report a bug, you need to isolate it. If you were to present developers with this complex and large file, and say "there's a problem on layer 2", they will not like to find the problem. But hopefully we can help isolate the problem.
So far, I've discovered at least one troublesome object, and when I delete it, Layer 2 displays again. It's path 3688. It has hundreds of nodes (500something, iirc), and also has Powerstroke applied to it. (That might be too many nodes to expect powerstroke to function??)
Here's what I did.
-- hide all layers
-- unhide layer 2
-- Shift + Tab 4 times - normal behavior
-- Shift + Tab the 5th time selects the troublesome object. I know it's a troublesome object, even though I can't see it, because when it becomes selected, the scrollbars shrink as small as they can go, which means this object is HUGE (1000000.000 mm, which is as high as Inkscape can measure, I think). It probably is literally covering up everything else!
So I deleted it, refocused the canvas to the page border, and there's all of layer 2!
I don't think we have enough information to know if there is a bug which caused that object to become so large. Not unless you specifically remember what you did to it. It would have been the 5th to last object you created (Shift + Tab selects in backwards order, while just Tab select from the first object).
I'm thinking, with everything else you have in the file, losing that one object will not be a huge loss. I did try to edit it, but it's so huge, I couldn't find any Selection handles or nodes. Tried using the control bar, but the W and H fields are unresponsive. Probably you should think about breaking up this file into several separate files, since it really is quite large. You must be having some performance issues with it anyway?
Ok, I tried one last thing, to edit the object. But it just won't edit. I think you may have hit some kind of bug with the powerstroke. But without being about to provide specific steps which reproduce the problem every time, it won't be helpful to developers, to report it.
Edit
But if you can reproduce it, where there's only one object in the file (or 2 or 3, if needed to create the problem), let us know how, and we can test