If you you upgraded a Dirsync Server to the newer WAAD sync tool and the original configuration was syncing the full AD forest then when you upgrade to the newer version. You need to perform a full synchronisation with the complete AD Forest.
After the full sync completes , You can then filter the OU's and they will be deleted from Syncing with Office365.
I recently had an issue whereby the objects in the OU's that I had filtered were not getting removed from my Office365 tenant. So to resolve the issue , I performed the steps above.
Once complete , Run the powershell command below to clear out the Office365 recycle bin.
Get-MsolUser –all -ReturnDeletedUsers | Remove-MsolUser -RemoveFromRecycleBin -Force