The files are copied via a temporary folder on your local Windows system. Windows file system is case insensitive. So the files overwrite one another. You have to copy the files one by one.
Even better is to avoid having files with the same name, except for the case.

Hi all,
I had a folder on a remote server (probably Unix/Linux) containing 2 files, among others: verify.py and Verify.py. I selected everything in this folder, right clicked, and hit Duplicate to copy it to another location on the same server. I selected Duplicate Via Local Temporary Copy because it has issues if I don't. It appears to download all the files to the temporary location and then reupload everything to the new place on the server. But Verify.py did not copy to the new location, but verify.py did.
Thanks