SharePoint Library Sync Limit

Need some help. I have a client who has 8 employees. I recently setup their Sharepoint online to do some basic document storage. They have 4 sharepoint sites and in each site they have like 3 or 2 libraries to avoid hitting the 5000 items limit for sharepoint document libraries.
Since migrating documents to the libraries, client has experienced issue with libraries refusing to stop syncing. i.e. the One drive for business keeps saying syncing 6323 items. Its been like that for days.
I researched and discovered that Microsoft has a limit on the number of items in total that can be synced across all libraries. i.e. 20,000 items. Check that here https://support.microsoft.com/en-us/kb/2933738
How do I get around that? Is there something I am not getting? Does it mean if you have 100,000 items in your sharepoint Online site document libraries you can only sync 20,000?

Thanks guys,