Clustered indexers have a 'cluster master' (CM) that manage their configuration files. So a hybrid set-up is going to complicate things with respect to configuration file precedence and overall management. Ideally, you'd migrate the existing configurations to the CM.
If you're going to convert, I would suggest setting up a set of small test VMs with IDXes having existing data, and convert them to familiarize yourself with the process. Testing is going to be especially important if you want to migrate your existing configurations to the cluster, since I doubt that the two IDXes have consistent configurations right now, given the partitioning scheme.
As for the partitioning aspect, do you have a UNIX system administrator in your organization? If so, you might want to sit down with him/her and discuss your requirements. Since you are in a VM situation, you could get a small-ish partition (20GB or so), and mount that at a temporary mount point, move /opt/splunk excluding /opt/splunk/var/lib to the new, smaller partition (or copy to new and then delete old). Then change /etc/fstab to mount the new partition at /opt ; mount the existing partition at /opt/splunk/var/lib .
Essentially, *NIX doesn't care where a partition is mounted; you just need to make sure when you set the fsck order that partitions that are closer to root are have lower fsck numbers, since the system can't mount the partition until the fsck is complete.
Is it possible to build new systems with consistent partitioning and migrate the data over to them? That might be cleaner, overall. It would consume temporary resources but allow you to release the existing resources when the migration is completed.
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