The IRS isn't trustworthy, even for for a government entity. In this day and age, the government shouldn't just "lose" emails.
Given how creaky the IRS has been with its efforts to computerize, I doubt the IRS is in this day and age.
Yeah, the OP lost me when he used the phrase "advanced computer systems" in conjunction with the IRS. It's hardly the first place to get a big computer update budget, especially given Republican efforts to starve the agency and privatize functions throughout the last decade.
It's highly believable that the IRS could lose emails. It's even more believable that the agency doesn't have the IT department resources to recover them once they're lost.