You could consider removing grants from the reporting tables while the load is running and only replacing them when the load has finished successfully. This would cause the scheduled reports to fail if the load has not completed successfully, but would not require any intervention on your part to log in and stop/start servers (although this can also be automated). In addition it would stop users from manually running reports against the incomplete data sets.
Once the load completed successfully, you could check for all the reports that failed and easily see which ones needed to be re-run.