You have a small mess that needs to be cleaned up. You may want to seek professional help in doing so.
The technically correct response is that you need to file all the returns using the correct EIN and these are all late. These returns should mirror what you have done previously using the incorrect EIN.
Then you need to amend all the returns filed that used the incorrect EIN to show zero on everything.
You will most likely receive late filing notices and penalties. Seeking professional help here may provide some assistance in addressing the late filing penalties and the correspondence with the IRS on this matter.
If would be helpful to understand why you have two EIN's and this may change my response.
Since you are responding from the TT Business software I assume that this is a multi-member LLC.
*A reminder that posts in a forum such as this do not constitute tax advice.
Also keep in mind the date of replies, as tax law changes.
