It all uploaded to the Clarivate server OK, but the other two Mac I use and that sync with my library became unusable (hanging, crashing…) as they were trying to download the changes. I made lots of changes to my library for instance. Other factors can affect performances too.
Now… that might not be the root cause of your issues on your Mac, but it might be worth investigating. I have the sidebar set to “Right - Preview” and now I can again scroll, search etc without having the app beachball all the time. I managed to regain somewhat control of the app though by simply choosing NOT to display the PDFs on the sidebar at all.
In essence, PDFKit has some significant issues and since EndNote relies heavily on them, the performances drop to a crawl any time a PDF is involved. I contacted Clarivate and they mentioned that it was due to the changes in PDFKit in Mojave. I have fewer references than you do (3700 - most of them with PDF attachments), but I was experiencing the same types of issues.
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