Upgrading from 4.7.x-1.0 to 1.1 - database

For some reason, I haven't upgraded the link module along with my other CCK modules. I was stuck on version 4.7x-1.0. Now, when I try to upgrade (to database schema 1), I get the following errors and all existing entries get lost and I can no longer add data using the fields. But the fields do display in the node edit form and I can do all sorts things with them in CCK field management. I would appreciate any assistance with making the switch. If there some way I could transfer these fields with a direct database query? It isn't too much data but it is enough to make me dread having to re-type it manually after an upgrade. This is the last issue I need to resolve before moving my site to 5.1.

    * user warning: Duplicate entry '362' for key 1 query: INSERT INTO node_content_journal_editorship (vid, nid, field_institution_website_url, field_institution_website_title, field_institution_website_attributes) SELECT vid, nid, field_url, field_title, attributes FROM node_field_link_data WHERE field_name = 'field_institution_website' in /var/www/eduweb47/includes/database.mysql.inc on line 121.
    * user warning: Duplicate entry '80' for key 1 query: INSERT INTO node_content_conference (vid, nid, field_project_website_url, field_project_website_title, field_project_website_attributes) SELECT vid, nid, field_url, field_title, attributes FROM node_field_link_data WHERE field_name = 'field_project_website' in /var/www/eduweb47/includes/database.mysql.inc on line 121.
    * user warning: Duplicate entry '333' for key 1 query: INSERT INTO node_content_user_profile (vid, nid, field_personal_website_url, field_personal_website_title, field_personal_website_attributes) SELECT vid, nid, field_url, field_title, attributes FROM node_field_link_data WHERE field_name = 'field_personal_website' in /var/www/eduweb47/includes/database.mysql.inc on line 121.