Batch merge automation of big data set
For big imports, I wouldn't use the UI and write either a custom script (using the API), using existing drupal modules (civimigrate or use an ETL (amnesty spain has shared a plugin for pentaho for instance)

It would likely be faster than trying to untangle where you are now.

If you can't start, I wouldn't try to merge the contacts, that is a complex operation, but simply write a script to identify the duplicates and manually update the individual to replace the "empty" organisation by the real record, and delete the empty record.

You can use the api from a php script that you'd run from the shell, it will be much faster to run than a "real" dedupe

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