Comment 11 for bug 916525

> he recovery file had only one layer, and all the elements of
> both layers were grouped (apparently one group for each layer)

Could it be that you (inadvertently) imported the emergency-saved file into an empty document instead of opening it itself?

Known issue:
Bug #502075 “Import Inkscape SVG loses layer and sub-layer information”
<https://bugs.launchpad.net/inkscape/+bug/502075>