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If an end user uses the "Upload a file" workflow in the HealthVault shell (https://account.healthvault.com/viewitems.aspx?typeid=bd0403c5-4ae2-4b0e-a8db-1888678e4528&additem=True) to upload a CCR or CCD file, the HealthVault shell recognizes that the file is a CCR or CCD and stores a CCR or CCD item to the record instead of storing a File item.
This logic is part of the Shell and gets exercised at the application layer. So if you write your own application which writes new File items to a HealthVault record, this logic will not get applied to your uploads. CCR or CCD files that you write with the File typeId will get stored as Files.
In a nutshell: the Shell can recognize that what the user thought was a File should really be stored as a CCR/CCD. The platform does not perform this check before storing a File item.