Microsoft published a patch for OneDrive for Business and I described the KB 2899513 here. Now I have seen, there is one more patch (KB 2899510) for OneDrive for Business, but not for the groove.exe. There are more files affected:
This update fixes some other errors in the synchronization of more than 10000 files:
Assume that you sync more than 10,000 files to your OneDrive for Business library. When you run the Repair or Stop syncing folder function in OneDrive for Business, you may receive many red X. Additionally, many files in the library are broken.
After you stop OneDrive for Business from syncing to a document library, you cannot open the document library in OneDrive for Business.
Assume that you are syncing OneDrive files locally on a Windows 8.1-based device. When you edit an Office document from that OneDrive folder in Word, Excel, PowerPoint or Visio, saving takes longer than expected.
Improves OneDrive for Business so that it can synchronize to an Information Rights Management (IRM) protected SharePoint library.
Improves the performance of the Office Document Cache by reducing the number of compaction tasks.
Improves the diagnostics for Office 2013 applications by logging the telemetry calls in the debug logs.