Looking at the commvault documentation, below:
...the only bit which comes close to the issue of file discrepancies, is the 'verify synthetic full backup' option which states:
"In a scenario where a conventional full backup is run only once for a given subclient, and incrementals (or differentials) with periodic synthetic full backups are run after that, files that never change may inadvertently be missed. Eventually, these files may be pruned, leaving no existing backups of the files. The problem of omissions may build up over time until the file changes or a conventional backup is executed. This can be avoided by using the Verify Synthetic Full advanced backup option.
When this option is selected, disparities between actual files on the client computer and the Index are collected. Internally, a flag is set when the synthetic full backup completes successfully. This flag adds functionality to the next incremental/differential backup to detect any items that the previous synthetic full backup did not include, and include any such items in that incremental/differential backup. The pending flag is cleared when the incremental/differential backup completes successfully, or when a conventional full backup completes, whichever occurs first"
However, there is no mention of 'deleted' files in the points above. It only seems to refer to files that may have been missed/skipped between backups (perhaps because they were in use etc)
I guess it's possible the 'verify synthetic full' option DOES index deleted files, and perhaps remove them when it builds a new synthetic full, although this certainly isn't clear from the documentation.
Anyone know the answer to this?