Greetings gmillow,
Sorry to hear about your EndNoteSync issue! Typically, I’ve found that closing/reopening the EndNote application will resolve this particular EndNoteSync error message. However, if doesn’t work for you, we should be able to workaround the issue by creating a new desktop library to sync with. You can do so by choosing File>New… within EndNote itself. Please be sure to give this new library a unique name, and make certain that you’re not saving the library with a folder that is being synced by another utility. Once the new library window appears, you can click Tools>Sync, then accept the warning indicating that you’re attempting to sync a library that is different than the last.
Please let me know if this works for you.