You found it right.
Maybe you are using background transfers and you need to uncheck No confirmations for background transfers?
https://winscp.net/eng/docs/ui_pref_background

I accidentally checked the "Never ask me again" box when uploading. Now, I want it back, but I cannot find where to re-enable it. The Preferences->Environment->Confirmations->Overwriting of Files box is checked, but it still does not show up. It simply overwrites automatically.

How can I re-enable this setting?

Thanks