When the file was accidentally renamed to “.”, the current directory was forcibly removed

As per the subject,

When the file was accidentally renamed to “.”, the current directory was forcibly removed.

Tested on a few servers.

Current WinSCP version: 6.5.6

That's expected. Just that by default, you would get a warning saying:

Directory '.' already exists. Overwrite?
All files in the target directory will be deleted!

You probably have overwrite confirmations disabled. Re-enable them if you want to we warned:
https://winscp.net/eng/docs/ui_pref_environment