We are utilizing Performance Monitor on a Win Server 2012. There are two collector sets that apparently were created when we installed Exchange 2013. I've modified both to send the output files and reports to a shared drive, and also adjusted the counters and sample intervals to manage the relevance and size of the logs. When the server is re-booted for maintenance, the settings revert back to what they were prior to my modifications, i.e. the output files and reports are pointed back to the local C: drive, the full counter lists are restored, etc. I've searched TechNet and EE, but have not been able to find a solution.
http://windowsitpro.com/blog/exchange-2013-diagnostic-and-performance-log-files
Mahesh