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Missing folders in Server 2008 R2 after Raid controller update.

I have a very strange issue going on. I am not sure if this is the cause, but we applied a RAID controller update on the server and scheduled it to reboot. The following day people said they could not connect to their shares. When I log onto the server, I cannot see the shared folders. It's like they disappeared. strange thing is I can view the files/folders if I actually type in the path of the folder. So it's like they are still on the server, but it does not show through "computer" and clicking on the drive. It is a Windows 2008 R2 SP1 enterprise. 12Gb ram and plenty of hard drive space. it is a DC and the only one in the domain. the folders are not hidden. I am at a loss of what to check.
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atisw
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atisw
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theras2000Commented:
You've said this in a bit of a confusing way.  You said:
1. When I log onto the server, I cannot see the shared folders
2. I can view the files/folders if I actually type in the path of the folder
3. it does not show through "computer" and clicking on the drive

What is the path of 1 of these folders e.g. d:\folder1?
What should the share path be e.g. \\computer1\share1?
Are you able to see the files by going to d: and clicking on folder1?
If you go to the properties of folder1, can you see the share details?
On the server, go to Run and type in compmgmt.msc.  Go to System Tools, Shared Folders, Shares.  Do you see them there?

Apart from those questions, I'm going to take a guess at what's really happening.  I think you're able to see the data via the local paths e.g. d:\folder1 but not via share names e.g. \\computer1\share1.  I suspect that Windows thinks they're new drives, so it's lost the information about which folders were shared.  If this is true, you'll have to recreate each share again.
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atiswAuthor Commented:
Yeah, I am really confused....sorry. This is what is happening....

if i am logged in to a workstation I can see the files and folders by going to \\server\Apps. inside the Apps folder the structure is missing. there are files in there, but missing folders. If i type the path \\server\Apps\folder..I can see what is inside. i have to type the whole path of the folder to see it.

if I log into the server.. i cannot even see the the folders that are shared. But if i go to D:\data\apps\folder I can view the files in that folder. Its the strangest thing I have ever seen. The files are there.. you just cant see them ...only by typing the full path.
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atiswAuthor Commented:
Another thing I noticed..I am running a Av scan right now and it is scanning the folders that seem to be non-existent.
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atiswAuthor Commented:
I can also see the shares from computer management. I can get into the properties of the share. I'll probably have to call the manufacturer as nobody understands what I am seeing. atisw is a support team. Was told that a bios update, raid controller update, and some firmware update were applied all at the same time. I believe problem started after reboot to apply the bios, fw, etc. who knows what happened. if you have any insight on what i should check, let me know as I am desperate to get things working.
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theras2000Commented:
OK so clearly the data is there, and it sounds like you're only able to browse directly too each folder if you know the path, rather than navigate to it by clicking.Are yoou logged in as an admin user?  Can you examine the NTFS permissions on the top weird folder and see if everything looks normal?  Can you try creating some new oflders and see if this happens there too?
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atiswAuthor Commented:
Yes, it is there and yes you can only view the files if you know the path. I am logged in as domain admin. I can see that the ntfs and share permissions are normal as what I had originally set them to. i created a folder, put a file in it and shared it. Seems normal. We originally thought all the files were gone so we started a file restore. I noticed it was restoring files to the locations i still cannot see. The backup sees it..the av sees it. why can't I???
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theras2000Commented:
Oh wait, it's not something as simple as hidden folders is it?  You could check the properties of the folders and the folder options in the View menu of Windows Explorer.
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atiswAuthor Commented:
That was the first thing i though too...My folder view shows hidden files...
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theras2000Commented:
I really don't know.  It sounds so strange.  Perhaps some kind of error in the new driver.  Can you try finding a small subfolder and copying it to: the same locatoin, another location, the root, another server, a usb stick etc. etc.  See if the invisibility remains.
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atiswAuthor Commented:
Wait...you are on to something here.. I selected show protected operating files and now I can see them. how do i make them not protected files. do you know?
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theras2000Commented:
Well ... I know how to do it in a CMD prompt from way back in the day.  It still works ...
Do some testing in small amounts until you're comfortable with this.
Try these commands below, 1 at a time, which create a folder, then view all system files both before and after making the folder a system file.

md aaa
dir /a:s
attrib +S aaa
dir /a:s
attrib -S aaa
dir /a:s
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atiswAuthor Commented:
It all makes sense now. I believe this is virus related and nothing to do with our firmware updates. I checked the ESET log and real-time scanner found infected items in some of these folders from a particular user today! The virus must have set the file attributes on the folders she was accessing. I think I can get this. I have used attrib many of times actually, but it's been awhile. Thanks for your help. I will post more info once i got it all figured out.
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atiswAuthor Commented:
Thank you for pointing me in the right direction. I did check hidden folders, but not system protected. ran Attrib -h -s on the folders. Fixed the issue.
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theras2000Commented:
Fab!
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