Folders and Files Disappeared

Unless they were securely deleted, deleted files are still restorable if only a little amount of data was written to the hard drive (saving files, watching videos, etc.) after they were deleted. When you (or Windows or whatever in this case) delete files, they really just become invisible and are restorable - until your hard drive needs to make space for a new file in which case the invisible file is overwritten/replaced.

Unfortunately, if Windows deleted the files before performing the upgrade, the vast number of file operations that took place during the upgrade probably caused it to be overwritten, but it's still worth a shot!