Currently we are using SHA1 signed certificate to our Jira tool/version(6.3.6a) and It will have issues on the 1st January 2017 and needs to be regenerated.
Could you please provide guideline to be regenerated this?
Not sure if you mean the certificate for running it over SSL or for it accessing SSL protected services.
See https://confluence.atlassian.com/adminjiraserver071/running-jira-applications-over-ssl-or-https-802593051.html or https://confluence.atlassian.com/jira/connecting-to-ssl-services-117455.html depending on which it is.
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