Since ios6, itunes deleted all my songs on my ipod and on my computer!

Question

I have itunes set to organize my library for me. I found that for some reason after ios6 update, when I synced my ipod, all of the music got removed from it. However, at the time, I could still play it on the computer.
When I looked into the itunes folder, I found that when I played a song on my computer, itunes would copy that song from its original location in the itunes>music> (artist name) folder to another folder it created in itunes>(artist name). In other words, it was moving everything out of the music subfolder into the general itunes folder. Everything that it moved would subsequently sync fine to the ipod.
So, thinking I had the solution, I told itunes to consolidate my files in my library. Apprently bad idea. It did copy all of the files from within the music folder out into the general itunes folder, but somewhere in the copy, it must have lost the files, because now most of them are no longer on the computer either. When I go to play them in itunes now, there is an exclamation point. Itunes deleted my music and instead, I have folders with artists name, and a placeholder of sorts where the file is supposed to be with a little x over it (Ihave windows 7, btw). Nor are the files in their original folders in the music subfolder. I never touched any of this music manually. I was trusting itunes to do its thing with keeping my library organized and all.
It did manage to copy about 1000 of them just fine, but all the rest of my music is gone from my computer! I did also restore the ipod, which seemed to sync fine after the restore, but again, because of the now missing music on my computer, obviously those files did not sync. Help. What happenned????

Answer 1

Reset didn't work at first until I unchecked the 'sych only checked songs and videos' in iTunes, clicked apply and then rechecked it and clicked sync and it worked.
Thanks.