Need 64-bit version of Notepad ++ to edit applicationHost.config file in any 64-bit version of IIS
If you try to edit and save changes to applicationHost.config file in a 64-bit version of Internet Information Server, your changes will not be saved correctly with notepad++ 32-bit. If you login in with admin privileges, you can make changes to the file and save them, but it doesn’t same them in the correct place. It saves them in the 32 bit location, which is Windows\SysWOW64\inetsrv\Config, instead of the correct 64-bit location, Windows\System32\inetsrv\config. The only work around is to use a 64 bit editor, like notepad, which does come with the 64-bit servers. Is there any hope for a 64-bit version of notepad++? I just spent a couple days solving a problem because of this. There is no warning and it is not obvious.
in addition you could use the sysnative alias to edit the file.