In SciNote, you can archive your protocol (and other data) and recover any archived files or entire projects at any time, to make sure you do not loose anything.
For the time being, there is no option to completely deleting protocols in the Protocol repository, since that could mean deleting them for other users as well (for the ones invited to your team).
To archive a protocol follow these steps:
Select the protocol and click Archive.
When a window appears click Archive.
If you wish to restore the archived protocol, go to the Archive, select it and click Restore.