A deleted custom report shows up under Reports > Monitor Tab, as shown below:
To delete files in the custom report, run the following command:
> delete report custom scope <shared or VSYS #> report-name <Report-Name> file-name *
This will remove the deleted custom report from showing up in the Reports section.
I have a similar, but different issue.
I have a custom report that I have deleted from the "Manage Custom Reports" tab, and have cleared all old reports as described above; while this deletes the reports themselves, I get a "Server error : unable to remove directory for 'Test Report'" error from the command line, and the report is still showing up in 'Reports'.
Not only that but it's still running - so every day I get a new copy of the report being generated - it's as if an orphaned copy of the scheduled report has been created and is no longer available within the GUI to delete.
Is there any way from the command line UI to force-ably delete a scheduled report?