Systematic review software may offer this functionality, or you can use one of the following methods to remove duplicates from a merged EndNote library.
Before deduplicating, you will need a merged EndNote library containing the records from all your separate EndNote libraries for the individual database searches, if you had previously exported records from each database into separate libraries:
Using this merged library of records from your individual database searches, you are now ready to remove duplicates. Here are two methods you can use:
1) Earlier version of "Bramer method" for deduplicating, with steps provided in Word document format:
2) Paper describing more advanced configuration options for removing duplicates in EndNote: Bramer WM, Giustini D, de Jonge GB, Holland L, Bekhuis T. De-duplication of database search results for systematic reviews in EndNote. Journal of the Medical Library Association : JMLA. 2016;104(3):240-243. doi:10.3163/1536-5050.104.3.014
Create a compressed library for backup after having removed as many duplicates as possible, with a filename like SearchTerms-yyyymmdd-Deduplicated—xRecords.enlx. This will be the library for screening. You can export the deduplicated library to Rayyan (see Rayyan guide for information on proper format for the EndNote file), for example, or other synthesis software, to facilitate the screening process, which usually involves more than one reviewer.
Create a free account with CREBP SRA, log in and import your library (ideally with < 2000 if performing this online), and use the Deduplicate tool.
Keep a copy of the RIS or XML file for your records.
See also: Rathbone, J., Carter, M., Hoffmann, T., & Glasziou, P. (2015). Better Duplicate Detection for Systematic Reviewers: Evaluation of Systematic Review Assistant-Deduplication Module. Systematic Reviews, 4(1), 6. doi:10.1186/2046-4053-4-6