That option is off by default.
Your script may take a on-default configuration from WinSCP GUI.
You should better isolate your script from GUI configuration:
https://winscp.net/eng/docs/scripting#configuration

How do I set this in a script? And what exactly do I need to set?
To describe the complete set up: I want to use WinScp to backup multiple folders and to be able to restore them without overwriting the existing permissions :roll:

nickbe wrote:

I'm using a synchronize script via SCP, but I can use sftp if need be.

Make sure you have Set permissions transfer setting turned off:
https://winscp.net/eng/docs/ui_transfer_custom

martin wrote:

What protocol?
If SFTP, you may need to turn off Transfer Resume / Transfer to Temporary Filename:
https://winscp.net/eng/docs/resume#automatic
https://winscp.net/eng/docs/ui_pref_resume

I'm using a synchronize script via SCP, but I can use sftp if need be.

What protocol?
If SFTP, you may need to turn off Transfer Resume / Transfer to Temporary Filename:
https://winscp.net/eng/docs/resume#automatic
https://winscp.net/eng/docs/ui_pref_resume

Is it possible to tell WinSCP to retain all existing permissions when uploading files from local to remote. Especially when overwriting a file, how can I ensure that the resulting file has the same permissions afterwards.