Folder permission reset and missing folders or files

This issue only occurs once per month on an estimate.
When we come in to office in the morning, we will discover our folders permission has been reset and some files are missing.
When we use the restore previous version, we can still find the files or folders in the last SECOND version. The last version will shows some files missing. Usually the last version is after office hours. Is there any possible cause to this issue for example
DFS services, VSS services, etc?
We also found out, if there is a wrongly moved folder e.g c:\123 has been moved to c:\anotherfolder\123, the latest copy will also reflect the wrongly moved folder, e.g. c:\anotherfolder\123 instead of c:\123 (which is right)
This is just like as if the parent folder has been restored to a certain date by an unknown program.
Thank you

Hi,
Do you using a DFS share for that? If so, please refer to the article below to check if it helps:
The ACL permission of some DFS folders is incorrectly reset after you restart the DFS Namespace service in Windows Server 2008 or in Windows Server 2008 R2
http://support.microsoft.com/kb/2464365/en-us
You could configure auditing on the folder. Then you can go through the auditing log to check which process is doing on all these files. 
Auditing File Access on File Servers
http://blogs.technet.com/b/mspfe/archive/2013/08/27/auditing-file-access-on-file-servers.aspx
Best Regards,
Mandy 
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