File system error

Urgent.
 On one of Our servers, (2003 R2)  serving pc's and macs, several folders have turned into unreadable files.  The Virtual server runs on a Vsphere 4.1 platform, but no other server on the datacenter is experiencing this.
The files in question were worked on and altered this weekend, but my backup from Friday also shows files, and not folders as they should be. That means the damage occured earlier and the folders were still accessible in the network after the damage. (probably by some kind of caching)
Yesterday the server was restarted because some files was not showing on afp-shares. The same files showed nicely when accessed from samba. The restart might have been the point in time where the mentioned folders turned inaccessible. Even from the local OS on the server, these folderes now appears as files, named like the folders. I suspect that services for macintosh might be the culprit.

Any help would be greatly appreciated.
I haven't run chkdsk, as I'm afraid this may permanently alter the folders (files) and ruin my possibilities of recovery.
MrWhyAsked:
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MrWhyAuthor Commented:
This turned out to be a misunderstanding. The folders in question were not folders after all, but files. The files Resource fork in afp were goofed up by file services for macintosh, and that led to macs not recognising the files as quark documents. As I was informed that these should be folders, led to me investigating wrong paths. The filesystem is ok. The files are ok, they just need to get copied out from apple filesystem Resource fork hell via a samba share, and the are magically readable again.
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noxchoGlobal Support CoordinatorCommented:
Well done with keeping CHKDSK away. And you have right - this could do the things worse.
Your first step is to use recovery software in hope that files in good condition are still on the drive and could be recovered.
Scan the drive with GetDataBack www.runtime.org and see what you get.
If you decide to restore something - make sure that you do it to different drive. Not to this one which is affected.
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noxchoGlobal Support CoordinatorCommented:
:)
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MrWhyAuthor Commented:
Solved this myself
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