Splunk is installed on C:\ and E:\, with splunk-launch.conf pointing to E:..
However once I complete the upgrade, the indexes disappear from the Webpage Splunk > Settings > Indexes but the search is still working.
I can create a new index which ends up in E:\ but after creation it doesn't appear within Settings > Indexes.
Installed Files Integrity Checker: Unable to access or parse the contents of manifest file in SPLUNK_HOME directory. As a result, file integrity information is not available. Verify manifest file in SPLUNK_HOME directory is still present, and that the splunk service user context will have read-access.
Confirmed using same account which originally installed Splunk v6.6.2