1. You can update your Inkscape version, if you want to. We're at 0.92.3 already, you missed 3 intermediate versions.
2. There have been path effects applied previously to the paths that behave weirdly. But the indication as to *which* path effect that was has been deleted from the path data. Still, the shape that the path effect had created was still in the path data, along with the shape of the original path, without the effect applied. When the grouping is removed, somehow also the shape indication gets removed. So this is how it happened.
I have no idea how the path effect info had been removed from the paths. Did you do any manual edits via XML editor or via text editor on the SVG file?
Selecting the affected paths (find them by searching for "inkscape:original-d" in the Find dialog, make sure to check search in Attribute names and Properties), then doing Path -> Object to Path fixes the issue, and that's the only way it can work.