The IRS has updated the FAQ on the procedures to fax Forms 1045 and 1139 under temporary procedures.[1]

The IRS has updated the initial question describing how the process has changed:

1. How does the process change from the normal hard copy mailing requirement?

Previously, these forms could be filed only via hard copy delivered through the USPS or by a private delivery service. There are well-established procedures for processing the hard copy forms in order to provide quick tentative refunds to taxpayers. A temporary procedure to accept these forms via fax permits us to make the relief in the CARES Act available to taxpayers before IRS processing centers are able to reopen. The procedures to process claims generally remain the same, except as noted in these FAQs. (updated April 30, 2020)

The IRS added guidance to explain what will happen if a taxpayer needs to both file a Form 1040X or 1120X in order to modify or create an NOL after CARES Act changes and also wishes to file a Form 1045 or 1139:

9. What will happen if I filed a Form 1120-X/1040-X that has not been processed and I used those numbers in my Form 1139/1045 filing?

Your Form 1139/1045 must reflect your originally filed or previously processed amended information. If your Form 1139/1045 does not match your IRS account, the Form 1139/1045 cannot be processed because the Form 1120-X/1040-X needs to be processed first. For example, if you gave a Form 1120X/1040X to your examination team, it has not been processed.

Do not attempt to fax an amended return at the time of faxing Form 1139/1045. Amended returns will not be acted upon when faxed with Form 1139/1045 through the temporary procedures. (updated April 30, 2020)

The IRS expands on additional issues related to the combination of filing a regular amended return and a Form 1045 or 1139:

15.  If I need to amend my return by filing a hard copy Form 1120-X/1040-X through the mail (since fax is not available for these forms), can I still file a timely Form 1139/1045 for 2018 for which the time for filing is extended under Notice 2020-26?

Yes.  If you need to amend a previously filed return prior to filing Form 1139 or Form 1045, follow normal filing procedures by timely filing hard copy Forms 1120-X/1139 and hard copy Forms 1040-X/1045 as applicable, in order to adhere to any filing deadlines particular to your situation. (added April 30, 2020)

16. If I amend my return by filing Form 1120-X electronically, can I use these temporary procedures to file my Form 1139 using those amended amounts?

Yes. Please notate on the fax cover page that you e-filed Form 1120X and the date that it was accepted.  Please note that we will be unable to process your Form 1139 until the amended figures from the Form 1120X have been processed and reflected on your account.  The timeframe for processing the Form 1120-X and adjusting the account depends on the particular taxpayer’s circumstances.  Once our normal mailing operations resume, if your account has still not been adjusted and we are unable to process the Form 1139, we will mail you notification of this status. (added April 30, 2020)

The IRS also updated the warning about not giving a Form 1139 to an examining agent, adding Form 1045 to this guidance as well.

14. I am currently under examination. Can I give the Form 1139/1045 to the examiner?

No, you should not give the Form 1139/1045 to the examiner. You should file it via the normal process or via the temporary procedures outlined within. (updated April 30, 2020)

The revised FAQ adds guidance on how quickly taxpayers may expect to receive refunds when they file a Form 1045 or 1139 under the temporary procedures:

17. When can I expect to get a refund from a Form 1139 or 1045 that was faxed under these temporary procedures?

The statutory timeframe for processing these forms is 90 days.  The IRS is mindful of taxpayers’ need to get these refunds.  As a result, the IRS set up these temporary procedures to process these forms while our normal operations are closed due to the pandemic.  In order to do this, the IRS had to create new processes and procedures as well as get our skilled employees available and trained to work these cases remotely.  We are working to process these refunds as quickly as possible, with limited staffing, managing the volumes and adjusting to processing these refunds in a remote work environment. (added April 30, 2020)

Finally, the FAQ notes that no such fax procedures exist for carrying back a loss from a Form 990-T:

18.  May I use these temporary procedures to fax Form 1139 or 1045 to submit a tentative refund claim for either an NOL carryback or AMT credit associated with a previously filed Form 990-T?

No.  The organization must mail an amended Form 990-T to the address shown in the Instructions for Form 990-T; and may attach a Form 1139 or 1045 to the amended Form 990-T to show the computation of the refund claim. (added April 30, 2020)

[1] “Temporary procedures to fax certain Forms 1139 and 1045 due to COVID-19,” May 1, 2020 version, IRS Website, May 1, 2020, https://www.irs.gov/newsroom/temporary-procedures-to-fax-certain-forms-1139-and-1045-due-to-covid-19, (retrieved May 1, 2020)