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Please see this article for instructions Update EndNote to version EndNote X9.3.1 macOS Catalina will warn you
I have EndNote X9, how can I know if it’s OK to upgrade to macOS Catalina? However, if you upgrade to macOS Catalina, your older version of EndNote is not going to work. Yes, you may continue using your older version of EndNote with your existing macOS. I don’t have EndNote X9, can I keep using my existing version?
We do not recommend upgrading to Catalina with EndNote X8 and earlier as we expect major compatibility issues.