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You can check your library for duplicates at any time by clicking Organize tab, then clicking Find Duplicates in the secondary navigation. Any reference identified as a duplicate will have a yellow background. You can quickly check the 'Duplicates' checkbox to check all references with the yellow background to delete those references, move them or copy them to your Quick List.
When using Find Duplicates, EndNote online compares references based on the following fields:
If you make a custom selection of duplicates on the duplicates list and then navigate to view a reference, you will lose your selection.