How can I get the scp command to overwrite the destination folder

As said before, scp happily overwrites any file that is already present.

The "file exists" issue can only occur when you have some other process (like a concurrent scp process, or something else) writing folders and files to the same destination. Consider using rsync instead.

You will receive this error message if the destination directory already contains a file with the same name as the source directory you are attempting to transfer. You can not have a file with the same name as a directory in the same directory.

Like Levans, I have been unable to replicate this, but have you considered using rsync over ssh instead? If you're copying large numbers of files, rsync may be a better option than scp. There are a number of good guides to it online, such as these:

http://troy.jdmz.net/rsync/index.html https://calomel.org/rsync_tips.html

That first link deals with automated backups via cron, so some of the instructions (like creating an ssh key without a passphrase) may not be relevant to you.