EDIT:
just to save you from reading the rest which I already wrote earlier in this post.
>Files are all back and ALL are working correctly now!
All I did was to unplug the Disk and put it into a different (faster) external Box.
I guess windows still might have had the corrupted version of the filesystem cached. (I did not reboot after the checkdisk)
So thanks again for being so helpful!!!
===================================
Thanks to everyone.
Before I go the next step I just want to make sure one more time if I have phrased the question correctly and write down a few more details.
The real problem in this case is, that all the files that I am looking for "are basically there" as I mentioned in the first post. The problem is that the "contents" of many of these files are messed up - "swapped". For example there are contents of file "examplefile 1" visible when I open file "examplefile 3"
It's not like they were manually deleted and I am 99.9% certain that it's a disk hardware issue.
As I also mentioned I have successfully recovered lost files from HDs in the past - even rebuilt a lost RAID 0.
I have VERY rudimentary knowledge about file systems and from what I know the problem here is something like this.
Windows has some files that act like a index. this index tells it where to look when a file is opened. larger files are ususally fragmented into many smaller chunks. and the locations of these chunks are all recorded in some place.
in my case something like the following has happened:
When the last BSOD occured that I mentioned earlier, windows was writing to this index and a few parts got messed up. As a result some folders were missing in explorer. > The files are still there.... windows just did not know where they are located since the index was messed up. So I used Disk Check to fix this as I have often done in the past.
Now here comes the problem.
Windows "Fixed" all the lost files. I can see them all in explorer. its just that some of them contain the wrong data.
Recuva was actually the first program that I've used before I made the first post. But the thing is... and maybe I am making a mistake here because I havn't digged very deep yet -
Recuva doesn't seem to see any problem with the "lost" files. Because they are already there when I open recuva. They don't appear to be deleted or anything. So when I mark them for recovery it will just recover the same corrupted version - right?
Anyhow - if I have missed something please let me know