Internal indexes and summary indexes do not count against licensing hence are not captured in license logs.
I ran this in my test environment and can confirm that I dont see any of internal indexes or summary indexes.
Can you check if those missing indexes are summary indexes/internal indexes?
I can confirm that those are not summary/internal indexes.
Just checked license_usage.log file in Test Environment and found the following line:
11-28-2019 11:18:33.645 +0530 INFO LicenseUsage - type=Message - License usage logging not available for slave licensing instances, please see license_usage.log on license master=https://splunkl****:9089 for usage breakdown
We don't have privilege to forward the logs of license master to indexer(Test Environment) due to other country Rules and Regulations. Is there any other way to get total amount of data indexed per day?