IRS incorrectly changed fiscal year

What a pain. My small nonprofit organization's gross receipts have always been well under the threshold to have an annual return filing requirement. But with the 2006 law, we have an e-file requirement.
I haven't been able to use the e-file system as it's not set up to allow the taxpayer to correct this error. Nor is an organization allowed to file on paper if the e-file system cannot be used, unless it voluntarily files a complete return on Form 990.
The filing deadline for organizations that hadn't filed for three years with calendar year fiscal years (as well as those ending in January, February, March, and April) to avoid an adverse revocation of their recognition as being described as various nonprofits has been extended until Friday, October 15, 2010. So, naturally, IRS Exempt Organizations office has been extremely busy. I was in call queues of over an hour each, waiting to talk to three different people.
For those of you in the same boat, this is what I was told to do:
1) File 990-N with incorrect fiscal year. Anyone can use any of the electronic filing services to do this. Urban Institute National Center for Charitable Statistics electronic filing service allows free filings:
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2) To have IRS correct its records with regard to the fiscal year, write to:
Internal Revenue Service Atten: EO Entity MS 6273 Ogden, UT 84201
According to one of the IRS staffers, their database shows a return filed for calendar year 2000, which had the notice that the fiscal year changed. I'm the only one with the organization who would file returns, and I didn't file this one. I was told that I won't obtain the return even if I request it as it's been destroyed per law.
Does anyone know if I can request a transcript? Also, what database was the IRS staffer looking at that showed a filing for year 2000, and what other information is in there if the transcript has been purged? I'd like to see any information from this mysterious return IRS still has.
Reply to
Adam H. Kerman

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