You can no longer upload OBIEE RPD files using the Weblogic Enterprise Manager console. You now upload the RPD via a shell script, or windows batch file if uploading from a client machine.
Trial and error suggests copying the RPD file to the server, then running the upload script is safer and faster than attempting the upload remotely from a client machine running the OBIEE client / developer tools
There is a difference in syntax between 12c environment versions however.
The commands are listed below, and once you have set the environment i.e. $PATH and $MW_HOME environment variables should be-able to put the commands into a shells script to reuse.
12.2.1 Upload / Download
data-model-cmd.sh uploadrpd -I <path to rpd file> -W <rpd password> -U <user> -P <password> -SI ssi
data-model-cmd.sh downloadrpd -O <path to rpd file> -W <rpd password> -U <user> -P <password> -SI ssi -Y
12.2.2 Upload / Download
datamodel.sh uploadrpd -I <path to rpd file> -W <rpd password> -U <user> -P <password> -SI ssi
datamodel.sh downloadrpd -O <path to rpd file> -W <rpd password> -U <user> -P <password> -SI ssi