In the current version 2.x there is the confinement now implemented, that a configuration should always be consistent and activated in a consistent state. So the way to go is manipulate an configuration archive and then activate it. In my example WinSCP is used. Connection Settings are:
"Host name": <IP of control>
"Port number": 443 (standard TLS/SSL port for real hardware) or 8443 (for port forwarded ctrlX COREvirtual)
Standard path: /solutions/webdav/<name of archive> or /solutions/webdav/appdata (for active configuration)
WebDav access to archived EtherCat configuration
Same can be done via the ctrlX OS web UI. Then REST protocol is used:
REST access to archived EtherCat configuration
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