I traced an issue down on one of our servers to an incorrect section in the .config file for an AppPool. If I manually remove the section from the c:\inetpub\temp\AppPools\thisAppPool.config which relates to one specific asp file (let's say site/epub/webservice.asp) then the web services work fine. However, if I then change a setting in IIS Manager, it overwrites this and re-adds the incorrect section.
I know how I can specify settings around authentication etc at the Virtual Directory level, but not at the file level (other than by editing the config file, which then gets lost).
Any ideas how I can stop this problem returning (other than by never changing things in the IIS Manager!)?
OS is Windows Server 2008 R2, IIS7