If the "Blank Account Number" box is not checked on the draft Form 1099, then the account number will auto-generate once the user generates a final. However, if users do not want the account number to print on the finals, then the box must be checked. Note, the IRS does require that an account number appear, especially if the payee has more than one return.
Users are able to input his/her own account number directly on the draft Form 1099, even if the system already auto-generated the account number.
See below for further details.
1099-R Instructions:
Account Number
The account number is required if you have multiple accounts for a recipient for whom you are filing more than one Form 1099-R. Additionally, the IRS encourages you to designate an account number for all Forms 1099-Rs that you file. See part L in the General Instructions for Certain Information Returns.
General Instructions:
L. Account Number Box on Forms
Use the account number box on Forms 1097, 1098, 1099, 3921, 3922, and 5498 for an account number designation. The account number is required if you have multiple accounts for a recipient for whom you are filing more than one information return of the same type. Additionally, the IRS encourages you to include the recipient's account number on paper forms if your system of records uses the account number rather than the name or TIN for identification purposes. Also, the IRS will include the account number in future notices to you about backup withholding. See Pub. 1220 if you are filing electronically.
The account number may be a checking account number, savings account number, serial number, or any other number you assign to the payee that is unique and will distinguish the specific account. This number must not appear anywhere else on the form, and this box may not be used for any other item unless the separate instructions indicate otherwise. Using unique account numbers ensures that corrected information returns will be processed accurately.
If you are using window envelopes to mail statements to recipients and using reduced rate mail, be sure the account number does not appear in the window. The Postal Service may not accept these for reduced rate mail.