Since Cypress 3.1, when exporting patients we follow the instructions in QRDA Cat 1 r3.1 Introductory Material Section 3.4 for a patient that has a Negation Reason for not being treated for anything in that Value Set:

Some cases need to exclude all possibilities, not just that of a single formulation or specific procedure. One example is the general “no Antibiotic Medications for Pharyngitis” compared to the specific “no Amoxicillin 60 MG/ML Oral Suspension”. Another example is the general “no Hepatitis A Antigen Test” compared to the specific “no Hepatitis A virus Ab [Units/volume] in Serum by Immunoassay”.
In such cases, where no code exists in the Value Set Authority Center (VSAC) value set to represent the general concept, use all of the following steps:
    * Use code/[@nullFlavor="NA"]
    * Set code attribute code/sdtc:valueset="[VSAC value set OID]"
   
This section also mentions an "originalText" element that provides a human readable indication that an entire valueset is being negated.  This free text field is currently not implemented in Cypress at the moment. This will not affect your import tests.  Additionally, when evaluating an uploaded QRDA document, Cypress allows for the negation of a single code as well as the negation of an entire valueset.  Therefore, it would be ok for your system to submit the following <code code=”73830-2” codeSystem="2.16.840.1.113883.6.1" displayName="reason" codeSystemName="LOINC" /> to Cypress.