Move multiple sites into a new folder

I have 400+ sites within WinSCP and want to move them into one folder. Is there a way to do so?

There's no easy way, yet. You can vote the feature request here:
Issue 2041 – Allow operating with multiple sites on Login dialog

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Meanwhile, all you can do is to export the WinSCP configuration to an INI file and do some smart (regex-based?) search and replace of the section names. Something like:
(\[Sessions\\)(.*\])=>$1\folder$2
And then import back (after removing the HKCU\SOFTWARE\Martin Prikryl\WinSCP 2\Sessions registry key).
Be careful, backup the WinSCP registry before.