Unfortunately the client uses a JIRA professional with the JIRA internal user management and JIRA currently doesn’t support import of the project between two different versions (Ent – Pro).  I assume, there are more people out there having the same “problem”. It was a manual process but did work in the end.

Prepare the local JIRA installations:

• Install a local JIRA Enterprise – not using the inmemory database
• First create a backup from your JIRA installation and restore it on a local JIRA enterprise installation. Unfortunately you can not connect to the local jira enterprise as you most likely don’t the users and passwords.
  Note the users stored in crowd will not be part of the backup/restore.
• If you can connect to the local JIRA enterprise skip the next steps.
• Next install a local JIRA Professional and create an admin user. Connect to the local database and export the data of the table userbase. You need to know the password as it is stored in the database, in the encrypted format.
• Connect to the database of the local JIRA Enterprise and check if there are any users in the table userbase.
  
• Update the password of the admin user in the database or if the user is missing – create the user in the database table userbase using plain SQL.
• Now you should be able to connect to the local JIRA Enterprise installation

Cleanup the local JIRA Enterprise

• Switch off external user management
• Delete all other projects
• Delete users and groups which are not needed any more
• Delete any customizations or set it as default. Customizations are i.e.
  • workflows
  • permission schemes
  • issue types, screens and screen schemes
  • …
• Change the project configuration (of the only project left over)
  • Issue Security Scheme is set to None.
  • Field Configuration Scheme is set to System Default Field Configuration.
  • Issue Type Screen Scheme is set to Default Issue Type Screen Scheme.
  • Workflow Scheme is set to None.
  • Project Category is set to None.
• Create a backup of the JIRA Enterprise Installation
• Restore the backup into the local JIRA Professional
• Now configure the local JIRA Professional according to your needs

And you’re done with it.
Create a new Backup or project export and Import it into the JIRA Professional Version.

This process did work for us and I hope it will help you resolving this issue if it will arise.