I don't know of any free file recovery programs, but have a few guidelines for you that will help if things go wrong in the future.

Always make backups of the files on your computer. This will make the need of any file recovery programs disappear. And I dont mean using the back-up option of your antivirus etc.
A lot of things can happen to a harddisk, not just some files disappearing. You can get infected by a virus or similar. Or as a worst-case-scenario your harddisk can crash. After something like that has happened it is too late to do anything, exept maybe paying large ammounts of money to pay some repairshop to TRY and get SOME of them back. Also if your computer gets infected there is a big risk involved in backing up files after, since in a lot of cases you can't be really sure what parts are infected.

I must say that I have no idea why your files would completely disappear just from upgrading. It sound really strange to me, that finished downloads would just disappear because of an upgrade.

Did you get your upgrade from the official source ?

Also always use an up-to-date antivirus program and antispyware program. And always scan your downloads before trying to open them