We have been trying to setup multi-foundation on Oracle JDEdwards EnterpriseOne 9.0 and have run into some issues with package manifests and such. So, once in a 2 full packages for the same pathcode show up as deployed in the package assembly screen. So, since the package is deployed, you can not delete it. Below is the SQL statement that I use to mark the package as not deployed:
update sy900/f9603 set PHISPTF=0 where phpkgname='