http://wiki.splunk.com/Community:Run_multiple_Splunks_on_one_machine
The link above will take you to instructions on how to successfully configure & run multiple instances on a single machine. The problem you are encountering is a known behaviour on Mac OS X. In running the install package for the second time, the OS inadvertently clobbers the original install, removing files and directories.
Usually it will leave the '$SPLUNK_HOME/etc' and '$SPLUNK_HOME/var' directories intact, so your configurations & data should still exist, but the instance will not be in a usable state and the best option at this point is to move what is left aside, download the .tgx package, extract it to the desired location and move your configs and data back over.
Assuming your 2nd instance installed succesfully when you ran the .dmg that caused this problem, you should now have 2 instances on one machine. Please read the steps in the article linked above to ensure that there are no conflicts between the instances.
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