I wish I could help you, but alas, just an Apache user. :(
Is it possible it is a disk error as opposed to an IIS error? Perhaps something that Chkdsk (or something more sophisticated) would fix? While the directory isn't available, can you right click on the directory in Explorer and choose Properties to see how many files and bytes are contained in the directory? What about copying and pasting the directory somewhere else? (To at least salvage your PHP files)?
It seems to me that right now your main priority is to salvage all of your php files contained within the directory, and once you know you at least have them, then to use them to get the Intranet back up and working.
cscgal
The Queen of DaniWeb
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