Folders changes & system restore points gone after weird restore!

Hi, I need your help.

I'm running a Windows 7 64 bit.

Last week I was going through my game folders and renaming a few of them and adding more info (my folders were a mess, organization wise). I also installed some older games I had on hard drive, to see if I want them anymore. So quite a bit of installing and uninstalling was happening, like say 20 games or so in a week.

Then yesterday one old game would not uninstall (not showing up in control panel list of programs), and so I decided to use system restore as a way to uninstall it. I restored the system to about four days prior...then a weird thing happened. Some of my folders were divided in two, the folder with the old name and another with with the modified name. Like if originally had a folder named "chess games" which had couple days ago during my reorganizing effort renamed to "Fritz Chess 9", now I had both! But they were not exact copies. What was contained in the original folder was now randomly divided between these two folders, like one subfolder in one and the rest in the other.

Also, the there were other folders that some of the actual content was missing. Like the ISO file. If I have 50 game folders, about 15 were affected, either in the sense of having duplicates or having game files missing. I am not sure but I think this happened only (at least mostly) to folders that I had changed the title of recently. The other ones were fine.

What did I do?

-I tried to merge the game folders (the ones that had duplicates of sorts) but stopped half way, deciding to run antivirus and anti-malware and nothing significant was found.
-SFC/scannow did not find anything needing repair.
-Tdsskiller did not find anything.
-I tried undo system restore and nothing was fixed. System restore to a few days earlier and nothing was fixed.
-I went to safe mode, tried system restore to the very first point available and this time system restore did not even complete and said "No restore points have been created on your computer's system drive." Indeed it was right, despite me having dedicated 10% to it and not having changed the settings. To make sure system restore does work, I created a restore point manually and that seemed successful.
-I banged my head against the wall hoping I don't have to reinstall Windows (worst experience ever before) and that my computer is not gone insane but now I have a headache.

What should I do?

Thank you for your reply bigmck, unfortunately since the restore points are all gone, I can not do that anymore. At present I am trying to figure out what else was affected, because it's not only my game folders but also music, videos, etc, pretty much anything that I had during that time made changes to (if I had moved a music file around to a new folder or renamed a folder).