Hi @Ronny Wombat ,
System32 is an important file on Windows&Windows Server, it stores many .dll files which systems running need. Microsoft doesn't recommend any one change the permission to affect its security.
If you change the permissions of this folder just to let FSW monitor the application host.config file, first I suggest you to give up using FSW. File permissions are the main reason.
IIS provides other ways to log changes to the applicationhost.config file. Using Configuration History with IIS 7 and IIS 8(In IIS 7.0 and above, we resolved this problem by creating a service that monitors for changes to the master configuration file, ApplicationHost.config, and periodically creates snapshots to later retrieve if necessary.)
It stores all history files in C:\inetpub\history
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Best regards,
Bruce Zhang