The IRS is a very large organization with centralized computer systems. Completely scrubbing data would be a very difficult and time consuming process and would most certainly have to involve a number of lower and mid rank career employees. It is much more difficult than just deleting an email from the in box or formatting the hard drive on a laptop. I doubt if many managers have the skill to do the job and the career employees who might have the skill are not going to engage in an illegal conspiracy to save them. Every career employee involved in data management is very well aware of the hazard involved. A real investigating will detect any effort to scrub incriminating evidence.
True. Some local, unreplicted documents may be able to be scrubbed using the right technique. But anything that ran through a server gets backed up and there's a transaction log that shows who did what and when. There are a LOT of tentacles of replicated files (eg RAID), backups, transaction logs and system logs. It would take a significant effort to recall off-site backups and destroy them, scrub logs, and run special scrubbing utilities to write over deleted files so the fragments can't be recovered.