Create a compressed library for backup after having removed all duplicates, with a filename like SearchTerms-yyyymmdd-Deduplicated—xRecords.enlx. This will be the library for screening. You can export the deduplicated library to Rayyan, for example, or other synthesis software, to facilitate the screening process, which usually involves more than one reviewer.
Bramer et al. have published more detailed and developed instructions on how to remove duplicates from an EndNote library.