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, with this new requirement by the IRS you will need to enter each form separately if they contain different CUSIP numbers.
Per the IRS Instructions for Form 1099-INT
Box 12. 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. If the tax-exempt interest is reported in the aggregate for multiple bonds or accounts, enter "various". If a CUSIP number was not issued for the tax-exempt bond, leave box 12 blank.