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EndNote EndNote How To
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Not if you delete and replace them with the journal terms lists available?  

But you can export the terms list, manipulate it in excel carefully reversing those two columns and then reimport it, if you want to retain your journal lists.  I don’t know why the Pubmed connect file imports them incorrectly into the Journal and Alt Journal fields which is where the terms are updated into column one and two, when the those options are set in preferences. You (or Endnote) might be able to edit the connection file to import them in the opposite way.  I much prefer to upload a pre-existing terms list per the KB article rather than keeping the one auto generated.  

These instructions are copied from CrazyGecko’s reply in a long thread elsewhere: 

EDIT THE JOURNAL TERMS LIST (Make backups of both your EndNote library and term list files before proceeding)

  1. You can maintain one list by exporting the journal terms list file and using MS Excel to “switch” the Journal and Alternative Journal columns.  [Go to the toolbar, select Tools > Open Tools List > Journal Terms List; click the “ Lists” tab then the “Export List” button.]

  2. Launch MS Excel and open the journal terms file. In the Text Import Wizard, use the default settings and click the “Finish” button.

3.The exported journal terms list file displays the Alternative Journal column in the first position (Column A), and the Journal column in the second column (Column B). Just “drag” (or copy and paste” to reverse the columns.

  1. Save the file as a tabbed delimited text file then import the file into the term list (make sure you delete the existing list before importing).