I have the same question data is appending but old data and new data will be same some time so i am seeing less than 1,000 rows in MS sql live db and 10,000 rows in splunk which means 1000*10=10,000 but there should be 1,000 rows only as it is in ms sql i mean mirroring !:)
Have you considered a live db lookup instead of deleting and reindexing the data every few minutes?
If you can't do a live lookup, consider writing the data into the key value store instead of indexing it. There you can delete, update, etc.
For actually indexed data, delete and update aren't valid operations.