Ok, I'll consider that. Thanks.

Thanks for the clarification.

However, I noticed that several other SFTP clients do not allow renaming a file or directory to "." at all, and instead treat it as an invalid name.

Is there currently any option in WinSCP to disallow renaming files or directories to "." specifically? By right, the action is rename, not overwrite the file. If not, would such a safeguard be considered for a future version?

Thank you!

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 be warned:
https://winscp.net/eng/docs/ui_pref_environment

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