No, it's way more complicated, if you need to keep the directory structure.
See https://winscp.net/eng/docs/library_example_moves_files_keeping_directory_structure

Do we just change: synchronize remote "D:\Share\" "/users/OurUser/"
To: put -delete "D:\Share\" "/users/OurUser/"

Or: put -delete "D:\Share\*.*" "/users/OurUser/"

We are synchronizing files from our local Server to an SFTP Server every 5 min via Scheduled Task.

What do we need to change to keep the local and remote folder structure, upload files only and delete local files after?

This is our current script:

Batch file:
WinSCP.com /script=Upload2SFTP.txt

Upload2SFTP.txt:
open sftp://server.com -hostkey="ssh-rsa 1024 a3:63:9a:f9:33:90:91:97:f5:60:f2:c5:ba:c8:5d:04"
synchronize remote "D:\Share\" "/users/OurUser/"
exit