It’s possible to re-install Linux without losing your /home data even if it’s installed in a single partition. There are a couple of extra steps involved to achieve this but it’s not difficult. As always, keep your data backed up and current.
I used VirtualBox for years and it was a fine and stable piece of work. (I don’t use it anymore, though, so don’t have the latest news about it.)
If you lose your Downloads folder again you simply can create a new one in the proper location. It will be empty of course but the OS will recognize it. It looks for a folder (a.k.a. Directory) named Downloads (or Templates, or whatever) but there’s no special ID serial number attached AFAIK.