If the symlinked folder was already indexed by your SQLite instance then, yes, the Cloner will re-import it because it is unable to identify the source of the DICOMs.
If you absolutely don’t want to re-index everything and stick with the old indexer plugin, you should index the symlinked folder (which you are already doing) AND the previous SQLite storage directory. This way, you don’t need the cloner at all.
But I strongly recommend using the latest advanced-storage 
It’s quite easy to spin a few Orthancs → I would strongly recommend that you play with a test setup with a few files to repeat your scenarios such that you can analyze the final storage consumption and make sure all studies appear in the final destination…
Best,
Alain.