There were changes in indexes.conf specification from 6.4.3 to 6.5.1 and Splunk would've validated/updated the indexes.conf file during upgrade process. Check the migration log ($SplunkHome/var/log/splunk/migrationtimestmap.log) and search for indexes.conf.
great. I see in the log the following -
Copying '/opt/splunk/etc/system/local/indexes.conf' to '/opt/splunk/etc/system/local/indexes.conf.old' but nothing about modifying the file....
-rw-r--r--. 1 splnkstg dce 314 Jan 4 19:23 indexes.conf.old -rw-r--r--. 1 splnkstg splnkstg 313 Jan 4 19:23 indexes.conf
One byte less in the modified file.
$ diff indexes.conf.old indexes.conf 2d1 < 4d2 < maxTotalDataSizeMB = 500000 5a4 > maxTotalDataSizeMB = 500000 8d6 < maxTotalDataSizeMB = 500000 9a8 > maxTotalDataSizeMB = 500000 12d10 < maxTotalDataSizeMB = 500000 13a12 > maxTotalDataSizeMB = 500000 16d14 < maxTotalDataSizeMB = 500000 17a16 > maxTotalDataSizeMB = 500000
I believe there was nothing changed on data perspective, may be some leading/trailing spaces got truncated. So basically you didn't have any incompatible indexes.conf entries so nothing new got updated, seems like it just created a backup and validated the stanzas as per 6.5.1 specification.
We had that happened when doing a Splunk upgrade from 6.4.3 to 6.5.0 on SBOX 1.4 - which was confirmed as a SBOX bug....
Hope this helps ...