You can make the file read-only to prevent automatic saving.
Hello,
Due to the sheer number of computers I use I like to store my three primary pieces of software (WinSCP, Notepad2 and PuTTY Tray) in my subversion repository and simply maintain a checked out version of this on every account that I use. This works seamlessly with the sole exception of the WinSCP configuration file, since it is automatically saved on exit one has to first revert it before updating the repository. Under normal circumstances the changes to the software configuration are not of relevance and can be reverted without consequence.
My proposal is an option that allows you to disable WinSCP's auto save on exit of the configuration file, and have an option that allows you to manually save the configuration file - like other pieces of software do.
Thanks!