The update did not delete your data, preferences or information but rather likely just misplaced them. Firefox stores all your information such as the data in your download folders in your Firefox profile. If you have important information from an old Firefox profile, such as bookmarks, passwords, or user preferences, you can transfer that information to a new Firefox profile by copying the associated files. The following link will provide you with detailed, specific instructions for recovering and or copying data from an older profile to the current or new profile in use.

See: Recover important data from an old profile

Are you sure that cleanup software didn't remove those downloaded files?

If "Open" and "Open Containing Folder" of an item in the Download Manager are grayed then that means that the files are no longer present in the original download location.
They may have been deleted or moved to another folder, but Firefox doesn't do such a cleanup.