Hi there,
I also followed the suggested steps and sync started to work well, but suddenly I realised that the system was not only syncronizing but also litteraly throwing away part of my collection at the same time! 
My original library in the desktop had 199 references and 190k and what I got after sync was a library with 46 references and 43k… thank god I was prudent and made a compressed library beforehand, otherwise part of my work had been completely lost!..
Any ideas on why has this happened?
I’m using Endnote X7 (Endnote X7.4, Bld 8818) with Windows 7…