If you have Endnote Basic, you will never have to sync with anything, because you will only have access to the online part of Endnote. If you have Endnote Desktop, syncing will be a way to move references from your desktop version to your online account.
In the past, syncing Desktop with Endnote Online has meant that any .lib or .libx desktop file you sync will download all the references that you have in your online account every time you open it. If you are using different library files to keep references for different projects separate, you will therefore not want to sync all your files with Endnote Online.
We suggest that you make one Endnote Desktop library file your "designated sync" file. You can set that file to sync automatically with Endnote Online, and keep any references you may want to save in there. For other library files on your desktop, we suggest that you disable automatic syncing with Endnote Online (see next box).
To disable automatic syncing between your desktop and online Endnote accounts, do the following: