Currently imports support is broken in OE.
OE will merge ontologies on processing an import directive, rather than import them. The user has to explicitly de-merge using complex save filters.
Fixing this will be hard. OE was not constructed to be aware of multiple ontologies.
This is unlikely to be fixed soon, as it will involve considerable code refactoring. Support will be in the form of the ontology-release-manager, an external tool. OE users will work with merged ontologies, the release manager will take care of de-merging and providing the correct output files with imports directives.
This tracker item is to show that the problem is acknowledged.