To disable taskbar flashing, run WinSCP once like this:

See https://winscp.net/eng/docs/rawconfig#flashtaskbar

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In the next version, I'll make the settings configurable in the GUI:
Issue 2411 – Make taskbar flashing configurable in GUI

Every time the server connection is lost, WinSCP pops up a notification. In Windows, the notification launches the taskbar, in my case normally hidden, and covers over a myriad of menus and toolbars disrupting my work flow. Is there a way to defeat, turn off these notifications. They are unnecessary and a constant annoyance. Other than this, I love the program.

Disconnected from server
Timeout (no operation for 1800 seconds)