C:\WindowsAzure\Logs\Plugins\Microsoft.Azure.Diagnostics.IaaSDiagnostics<DiagnosticsVersion>\WAD0107\Tables
Deletion should work if Monitoring Agent has already shut down.However, if deletion is not possible because of some files holding the lock, then disabling WAD first may help.
You can either uninstall the diagnostics settings extension from the portal and reinstall once you delete the files or stop the "Windows Azure guest Agent" service from the VM and perform the deletion action and then restart the "Windows Azure guest Agent" Service.
Please refer the below screen shots to disable diagnostic settings extension: