Just uncheck the Set permissions.
Please read documentation:
https://winscp.net/eng/docs/ui_transfer_custom#upload

I am using version 4.3.9 from a windows 7 host to a linux host.
When I upload files and scripts to the linux host, the file permissions are set per the transfer -> upload options -> set permissions. this is fine for simple text or data but not fine when updating or overwriting scripts that need to have the execute bit (x) set. I would like the ability to retain the permissions of the original file on the linux host if I am overwriting an existing file.