In case of SSL certificate errors, you may have to load certificate files in Java keystore. Here are instructions.
Instructions
Launch Service or Application URL in browser and downloaded certificate .cer file.
Import certificate in Java cacerts keystore.
First figure out JDK used by FlexDeploy and/or Endpoint as applicable.
For example, cd /u01/jdk1.8.0_60
cd jre/lib/security/
Copy .cer file in this folder.
cp cacerts cacerts.bak
../../bin/keytool -importcert -keystore cacerts -alias <alias name> -file <certificate file name>