A host was already sending data using an outputs.conf file . Another outputs.conf was added with out knowing which is linked to some other indexers. So what happens here ? Will it send the same to both groups or use the latest one or only the old one ?
This document addresses your question in detail.
https://docs.splunk.com/Documentation/Splunk/6.5.1/Admin/Wheretofindtheconfigurationfiles
AFAIK it will consider the outputs from an app that comes first in the alphabetical order.
For eg:
abc_outputs
xyz_outputs
abc_outputs will take precendence