I am not understanding where you are in EZ Pop. Your EZ pop output file will have a mutitude of columns each one is a designated field.

1) In your case a column called v_categories_name_1, 2, 3 etc... is relevant. You can clear out all data contained in any of these columns and/or replace it with some other data and upload it into your shop.

This will remove/migrate the items categories you overwrote. Worst case is it might dup them leaving the old category to manually delete.

but I don't think that would even be needed... just step 1. Pretty sure I have done this a million times and nearly certain it will just alter them and no dup.