Just so you understand the process. When you create a container in the plugin GUI two things happen:
1. That compose file is copied to the OMV database. The database is what the plugin uses to manage those compose files.
2. That compose file is copied to the storage path that you have defined in the settings tab. For backup purposes ONLY.
If you think about it you will understand what has happened to you.
Sounds clear but the import feature should be able to overwrite the current omv database with the one which is to be imported. Otherwise it becomes odd