when restarting the scheduling server, about 15 minutes later the DbCleanupThread will start doing its work.
So you can have a look in the server logfiles whether there is some error message related to the DbCleanupThread.
Try to set the server trace level to 2 so there is more information logged.
In addition please check the data using this query:
SELECT MIN(FINAL_TS) FROM SCI_SUBMITTED_ENTITY WHERE ID = MASTER_ID and STATE IN ('FINAL','CANCELLED')
Please do this a few days and compare to see if any data has been removed by the DbCleanupThread.
Please let me know the results and any possible error messages ion the logfiles regarding DbCleanupThread.