For anyone having the same problem this worked for me:
I opened EndNote-Online through the desktop version of Endnote (Help/EndnoteOnline) and logged in.
Went back to the Endnote desktop version and opened Sync-preference (Edit/Preferences…/Sync) and re-entered my password. Then pressed “Use”, and closed the preferences.
Now the sync worked again…
Not sure what caused this to work but i did…
Setup: PC, Windows 10, Endnote X9