The best way to do this and to avoid any possible inconsistencies with the CommServe Database would be to right click on the storage policy that contains the jobs that have been previously content indexed and view jobs. Once the list of jobs are seen, you can do select multiple jobs and delete them for content indexing. This will keep the backup intact for future restores and allow for normal pruning to occur.
Once the JOB id’s are deleted for CI the associated archive file references will be pruned periodically or start to prune when services on the CI engine are restarted. The periodic interval varies and depends on multiple factors, however it is approximately every 30 minutes