Of course that settings are stored in AppData. There else they would be stored? That's the designated location for user settings. You cannot write to Program Files, unless you run the application with Administrator privileges – what you should never do. Though if you want that, go ahead, then WinSCP will indeed write your settings there. But we do not recommend that.

WinSCP does not store the settings into any OneDrive folder. They are stored into C:\Users\username\AppData\Roaming\WinSCP.ini.
See also https://winscp.net/eng/docs/config#ini

This sounds fully like a OneDrive issue that WinSCP has zero control over.

OneDrive can cause file loss. It randomly strikes people. Even those who say its never happened to them for years, it randomly strikes too, and here and there they find out. Posts on this are found on the internet.

Removing OneDrive isn't difficult. Its one of the first things I do when setting up a clean OS. Uninstall OneDrive, and switch over the two or so Windows User folders via Windows registry that Windows sadly and oddly defaults to OneDrive. That's it. If you have problems before that, its not normal.

You should maintain 2 or 3 backups of all files, each backup should use different software, and you should keep an eye on them and test them for failures do happen especially with bad backup software. If you maintained proper backups you wouldn't have a problem here.

:)

After a recent upgrade, I found that WinSCP had completely lost all my sites! The obvious solution was to find the WinSCP.ini file, but I was surprised to find this stored in AppData rather than under Program Files. But the biggest shock was to find that WinSCP automatically stores the ini file in a OneDrive folder.

PLEASE never do this, and if Windows does it, please find a way do undo it. I have been trying to rid my computer of OneDrive for months now. I have unlinked it, uninstalled it and it still shows up. It is the cockroach of Windows.

Might I also suggest that you provide a search mechanism in your forum. In that way I can make a reasonable attempt to not duplicate existing requests, without slogging through a thousand existing entries.

But thank you for this product. I don't need it often but when I do use it, it has been a boon.