Not clear what you're asking. Are issuing the 1099 or receiving it? If issuing the 1099, I used the EIN for the disregarded LLC as the payer, even though instructions seem to expect my SSN to be used. Not sure what IRS could do to me for that.
Similarly, when the disregarded LLC was the 1099 recipient, I gave the payer the EIN on the W-9 even though the instructions say to use SSN. I don't think anyone had a problem with that, and the 1099 did get filed on my SSN account anyway even though it displayed the EIN.
