I see what you mean. Now that I've looked at your file for the 2nd time, and investigated further, I see that the Layers dialog is not displaying all the layers. But the Objects dialog does display them.
So you should be able to use the Objects dialog. Once I've unlocked everything from the Objects dialog, then I am able to select everythingin the root layer. I guess you could continue on, using the Objects dialog instead of Layers dialog. Except that keeping the Objects dialog is known to cause performance issues (slowness, maybe freezing).
But now, I'm actually not sure how this can be fixed. I'm not sure if these problems are related to the crash or a bug. You said there was a crash, right? Was it an Inkscape crash or your computer?
I've tried adding the missing layers back to the Layers dialog, but that results in duplicate layers in Objects dialog.
Oohh, I see how it works! Open the Objects dialog. Notice the column which is labelled "T". Those icons are so tiny it's hard to describe them. The icon which looks like an upside-down T is for "object". It never changes, as far as I can tell. The other icon, if you click on it, changes slightly. As far as I can tell, it just gets lighter, and very slightly larger. Unfortunately, that's the only way I can think to describe it.
When that icon is smaller, it apparently means Group. When you click on it to make it slightly bigger and ligher in color, it means "layer". When you click on a group icon and change it to layer, the layer suddenly shows up in the Layers dialog.
So what you'll need to do is go through the Objects dialog, and change your layers (some of which apparently where changed to groups) back to real layers. Keep the Layers dialog open at the same time, so you can verify that the change happened. And don't forget to click the tiny plus sign to expand the layers, because there are several sublayers as well. As soon as you click the icon in the T column to change it to the layer icon, it shows up in the Layers dialog.
Let us know if that fixes everything, or if there are any outstanding problems.