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Your Mendeley account gives you access to your Mendeley library via the desktop app and online. Synchronising the two means you’ll see the same references in either application.
At bottom of the black bar to the left of the screen is a 'Sync' icon (rotating arrows), which you can use to sync any changes you make to the cloud. It is important to remember to Sync your library, so that any changes are fully saved.
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When you open Mendeley Reference Manager, it will automatically synchronise with the web app and add any new references you have added there.
If you use the web app whilst the desktop app is open, you can tell it to synchronise by clicking on the Sync icon.