I have no real solution only some thoughts. Gimp .xcf files could be corrupted with large images and the image closed before saving was complete. The file totally unreadable. As far as I know that was fixed. You could open a "just saved" xcf and check for errors before closing the image and moving on to the next project.
A linked layer, is a reference to an external image. It allows the user to adjust the external image with some other program, save it, and the Gimp layer is updated automatically. I have tried adding a link layer, saving a xcf, closing Gimp, deleting the external image and it was still ok when I reopened in Gimp.
A couple of things to look at,
If you have any layer effects - That (fx) icons in the layers dock maybe flatten those before saving.
Layers larger than the canvas ? Then Image -> Fit Canvas to Layers.
I could only find those ancient posts about losing layers as well.
A linked layer, is a reference to an external image. It allows the user to adjust the external image with some other program, save it, and the Gimp layer is updated automatically. I have tried adding a link layer, saving a xcf, closing Gimp, deleting the external image and it was still ok when I reopened in Gimp.
A couple of things to look at,
If you have any layer effects - That (fx) icons in the layers dock maybe flatten those before saving.
Layers larger than the canvas ? Then Image -> Fit Canvas to Layers.
I could only find those ancient posts about losing layers as well.