If you receive multiple Forms 1099-INT or a statement with multiple accounts, and these accounts have different CUSIP numbers, you will need to enter a separate Form 1099-INT for each account. This is not an electronic filing requirement.
Although in the past you were able to consolidate Form 1099-INT entries on one form, the IRS now requires you to enter each form separately if they contain different CUSIP numbers.
Per the IRS Instructions for Form 1099-INT:
Box 14. Tax-Exempt Bond CUSIP No.
For single bonds or accounts containing a single bond, enter the CUSIP number of the tax-exempt bond for which tax-exempt interest is reported in box 8 or tax credit bond (including build America bond and specified tax credit bond) for which a tax credit or taxable interest, as applicable, is reported in box 1. Enter the CUSIP number of the bond for which interest was paid or tax credit was allowed. If the tax-exempt interest or the tax credit is reported in the aggregate for multiple bonds or accounts, enter “various.”