Sure, but the change in the end affected both operations.

I've reverted to the previous behavior for operations initiated by drag&drop:
https://github.com/winscp/winscp/commit/b3698f0078a3f3d71dade90fb0852799a00c5b55

Well Move to != Duplicate.
OK, I made a custom command with Rsync.

Yes, that's new behavior:
Issue 2209 – Improve behavior when moving/renaming over an existing folder
Currently, there's no way to "overwrite" a directory when duplicating anymore. You would have to delete the target directory before.

Remote Server OSes: Debian Almalinux Centos.

• Go to remote path /dir1
  
• Right click on dir2
  
• Duplicate
  
• Target remote path /dir1/dir2
  
• Modify to /dir4/dir2
  
• Copy /dir1/dir2 within /dir4/dir2 (/dir4/dir2/dir2)
  
• 6.1.2 and lower overwrites /dir4/dir2 with /dir1/dir2
  

Is there a new setting?
Dan