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Right. Took me a while to realize that background transfer has its own setting for overwriting! Should have posted here when I found that option. It works as desired now. Thanks!

I believe background because there is no popup that shows the progress.

Re: Overwrite confirmation not working on SFTP

Do you upload on foreground or background?

Overwrite confirmation not working on SFTP

I searched around the forum and saw a post where it is mentioned that the confirmation is not possible over SCP. But I am using SFTP.
Basically what happens is that... When I try to upload a file from my desktop to my Pi using WinSCP, the files on the Pi are overwritten without any confirmation popup.
I have checked the Preference > Environment > Overwriting of files and it is enabled.
I tried doing the same action on Filezilla and it does ask me for confirmation before overwrite so the feature does appear to be supported over SFTP. What could be the possible issue?