Windows – Entire Desktop Deleted

I cannot speak to the specific issue you are having (as I have never seen it do that), but Windows just does not have very good tools for managing or organizing icon positions on the desktop. Windows has neglected this since the very beginning. I personally keep icons in groups with gaps between them just to keep things mentally straight, but there are many actions which will cause Windows to just toss them all in the upper-left without regard to their previous positions.

You can try deleting your desktop.ini file. It's hidden by default but you can access it by showing hidden/system files, or by the command line. It will get recreated. You can also try deleting your iconcache.db file. It's located in your user profile folder under \AppData\Local (also hidden).

Normally I don't make product recommendations (especially commercial software), but in your case you might benefit from a program called Fences from StarDock. The program is free and allows you to group icons together and drag them around as a group. You can keep often-used icons together on one side of the screen and let downloads, etc. pile up however Windows does them on the other. It also preserves icon layout across resolution changes.