Files on our server disappeared after CC install

I'm hoping someone can help me figure out how to retrieve two folders that were deleted from our server after I installed full Creative Could suite on the iMac I use (designer) and InCopy on four editor computers (two PCs, two iMacs). The Macs are running Yosemite and the PCs Windows 7.
I now see from the discussion boards that this has happened in the past, but I hope to find out...
1. Is there a way to recover the files via Adobe?
2. How can I make sure this doesn't happen again?
The folders in question were named "Admin" and "Archives," so I suspect the problem was that Adobe had a conflict with the directory names. But since Admin stored our contracts and Archives had the past 5 years of our publication draft files, this is a big deal. (And wouldn't you know we discovered this morning that our backup had been failing for the past 2 weeks but no one told us. Grrr!)
Any help would be MUCH appreciated.

So embarrassed. Talked to Adobe support on the phone and then to our staff. It seems someone here DID get several pop-ups asking if it was okay to delete those folders and she assumed she should say Yes. At least the missing files affect her more than the rest of us... Needless to say, I have now turned off the file sync preference on everyone's computer!

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