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Sometimes you may need to move your main EndNote library to a different location or just decided to give it a fancier name at some point. However, after doing so, the EndNote software stops syncing that library. If you check with the preferences, you will find that the path to the synced library is still the old one and you can not edit it.

Actually EndNote saves this path in the registry in Windows. If this needs to be edited, run regedit and search for “SyncLibraryPath”. You can edit the text stored in that value to the new path of the library you want to sync with EndNote Web. On my computer this value resides in HKEY_USERS\S-1-5-21-3470660602-2923859688-2853976470-1001\SOFTWARE\ISI ResearchSoft\EndNote\Preferences , although I do not know whether that long string of number may vary on different computers.

Original solution: http://community.thomsonreuters.com/t5/EndNote-General/Not-syncing-with-endnote-web/m-p/61769#M10993