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The keystore.jks file in /etc/sdc is the keystore that is part of SDC itself. It's used by the web server providing access to the Data Collector via the UI or REST calls. That shouldn't be used for particular stages in particular pipelines.

What you need to do is add the certificate used by the server pipeline to its keystore, as well as the truststore for the client pipeline. To do this, you may need to create new keystore files (via keytool) in a directory you control that is accessible by SDC at runtime, and then import the certificates as required into those.