Nativity Certificate and Caste certificate are two very different documents.
While a nativity certificate is a government document which is issued by the State Governments to certify that the individual has been residing in a particular location for five or more years, a Caste Certificate is issued for the purpose of availing educational benefits, job benefits, and to avail various benefits under government schemes.
Nativity certificate is issued in every state in India and is used to get admission in schools and for employment purposes. For the purpose of creating a nativity certificate in Tamil Nadu, one needs to be a resident of Tamil Nadu and he/she needs to have any one of the following documents:
Hence for nativity certificate you only need to prove that you are a resident of Tamil Nadu. There is no need to worry as caste certificate is a completely different document and there is no issue of contradiction. Also, normally states have the caste certificates validity for 6 months to 1 year. In Pondicherry, the Govt has introduced the "Permanent Caste Certificate" which has legal validity for 15 years for educational and employment purposes. Hence, please check if your wife has permanent caste certificate or not.