Let's say you file Form SS-4 with the IRS, and then get impatient and call the IRS' toll-free phone number. Because you're dealing with two different IRS offices, there's a good chance the IRS will issue two different ID numbers for your business. If this happens, you must get the IRS to expunge the duplicate number from its records; otherwise they'll think you're operating two different businesses with the same name and will be looking for two different tax returns each year
To correct this problem, first call the IRS' toll-free number (866-816-2065). Explain the problem to the agent, and ask for the "entity fax number" for your regional IRS office. The agent will give you this number over the phone. You must then fax to this "entity fax number" a brief note explaining the discrepancy and telling the IRS which of the two numbers you plan to use for your business. The fax should be addressed to "BMF: Business Master File." Make sure the number you want the IRS to keep on file is the number you have used to open your checking account.
You should also mail "hard copies" of the fax to 1) the IRS office designated to issue your tax ID number and 2) the IRS office to which you're required to file your tax returns. Be sure to send these by certified or registered mail (so you get return receipts) to the attention of "BMF: Business Master File." It's not a perfect solution (the faxes may still get lost), but it's the best you can do.
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