When using the Schema Compare for Oracle (SCO) Command Line, you can make use of a SCO project file previously saved using the GUI, using the /project switch in place of the /source and /target switches as the data sources for a comparison.  For example:

sco.exe /project:"C:\Schema Compare for Oracle\MyProjects\MySchema.ocp" /verbose /Scriptfile:"C:\Schema Compare for Oracle\MyScripts\MySchema.sql" 

Upon reviewing the command line comparison, a message indicates that the objects are identical or no differences are found.

Any report you generate via the /report switch does not include any objects, and a deployment script generated using the /script:file switch does not include any CREATE, ALTER and DROP statements like this example script file:

To resolve this problem, you need to reopen the project within the SCO GUI and perform a comparison.  On completion, the comparison results view will be displayed.  You now need to select objects as if selecting them to be deployed.  Once either all the objects are selected or the required objects are selected, as per the image below, now save the project.