Yes, that happens. The IRS has a website where you can check which centers are able to file returns along with how many returns were affected by a site going down. If your return was not actually filed, you should file last year's return. You can do it before or after filing this year.
When filing this year, the IRS will show zero for the AGI for last year's return. Be sure to use zero for his AGI last year.
Reference: MEF status
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