In case of SSL certificate errors, you may have to load certificate files in Java keystore. Here are instructions.
Instructions
Launch application URL in browser and downloaded certificate .cer file.
Copy .cer file to server in jre/lib/security folder.
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/
cp cacerts cacerts.bak
../../bin/keytool -importcert -keystore cacerts -alias <alias name> -file <certificate file name>