The Use same settings next time is not for a current session only, it's persistent. But it applies to the settings above the checkbox only. So it particularly does not preserve the transfer settings. At all, not even for a current session.
The fact that checking the 'Use same settings next time' box does not work as expected. Next time WinSCP is started the latest changes are gone - as you already wrote. It will keep them only when doing this in the global dialog.
So WinSCP needs to make clear that this checkbox in the Sync dialog is a 'temporary' one.
I find this highly confusing as well. In the Synchronize dialog, why not change 'Use same options next time' to 'Use same options during this session', or 'Use these options until the session is exit'?
The 'Use same options next time' checkbox doesn't help.
I specify File mask in Synchronize - Transfer Settings, sychronize folders successfully but FileMask is empty when I open Synchronize dialog next time. It is only in the History. I have to open Transfer Settings each time and select File Mask.
Is it feature? Is it possible to specify the default file mask somewhere in the ini file?
WinSCP: 5.7 (portable)
OS: Windows 8