With just a bit of luck and a decent recovery program like Acronis, Ontrack, HandyRecovery, ZAR, QueTek, Cimaware, and 87 others, you can install your questionable hard drive in another desktop with the good drive jumpered as Master and the one with missing files and folders jumpered as Slave... and recovery anything that has not been overwritten.... so do NOT use that drive for anything until you attempt recovery.
You can also usually find the missing folders with regular tricks and use drag and drop to copy everything... Just be patient, and do the work while well rested and over the stress of the loss.
We rescue data for clients nearly every day, and it takes very little special expertise unless the data has been over written.