On some of our windows systems, the aps.net application may run as a separate user than your system / ftp user. if you require write access within your application, you can use impersonation and give the FTP user information as that will have the required write access. This can be done within the whole application or per code.
Please review the following Microsoft help doc for more info.
https://support.microsoft.com/en-us/help/306158/how-to-implement-impersonation-in-an-asp.net-application
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