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Make a backup of your EndNote library (or just copy the My EndNote Library.Data and My EndNote Library.enl) files somewhere else so you can use it to restore your library later.
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Open EndNote>Preferences>Sync and turn off automatic sync
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Quit EndNote
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Go to Users/[username]/Library/Preferences and find com.ThomsonResearchSoft.EndNote.plist
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Open the file in any text editor and scan through the mess for the “wrong” directory of your libary, replace it with the correct path, save the file, exit editor.
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Open Endnote>Preferences>Sync and turn on automatic sync, and use your account credentials
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Close Preferences, then go to Tools>Sync
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EndNote will now try to sync with the online account, you might lose a lot of references in this step, don’t panic.
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After EndNote finishes it’s long sync (retrieving references, sending updates bla bla), go to File>Open library and browse to the My EndNote Library.enl library that you saved at the first step.
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When it opens, select all the references, right click>copy references to and this time select your original library.
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After everyhting is copied, you might need to get rid of duplicates and sync the libary (maybe automatically) again.