I am just posting a solution to an issue I have had with two upgrades for Splunk Enterprise Security. First issue was when upgrading From 3.3 -> 4.0 and now 4.0 -> 4.1.
./splunk install app /tmp/einstall/splunk-enterprise-security_410.tgz -update 1
.\splunk.exe install app C:\SplunkUpgrade\splunk-enterprise-security_410.tgz -update 1
Then open your ES install and follow the prompts and it will work :).
View solution in original post