Hi,
to be honest, I’ve only ever had the launcher delete files when it fails ti install an update and, as mentioned before, I get around this by deleting my saved game, and then restoring it from the recycle bin.
If the launcher is failing because of a folder not being empty, try doing what I do, and keep files in an easily accessable place. In my case, I use a flash-drive that is always sat next to my PC… 