The storage on Office 365 OneDrive and OneDrive for business is no matter an issue
Earlier this year Microsoft has upgraded the OneDrive for business from 25 GB to 1 TB Check the news
Now Microsoft has break all the Storage rules and upgrade one more time to UNLIMITED storage
However this is not all of it , in fact, still a limitation for OneDrive. It’s a limitation that Microsoft is aware of, and one that Microsoft is working to address in the near future. But, for the time being, your OneDrive account can only handle 20,000 individual files
So the limitation change from the storage issue to the number of files , You can sync up to 20,000 items in your OneDrive for Business library, including folders and files.
OMG! Only 20,000 files per user? I already have 20,0001!
Number of items that can be synced
You can sync up to 20,000 items in your OneDrive for Business library. This includes folders and files.
You can sync up to 5,000 items in a SharePoint library. This includes folders and files. These are the libraries that you find on various SharePoint sites, such as team sites and community sites, libraries that other people created, or that you created from your Sites page. This also includes syncing other people’s OneDrive personal sites that you may have access to. You can sync multiple SharePoint libraries.
http://support.microsoft.com/kb/2933738