I would recommend that you complete the 3520 again and send it with a cover letter to the IRS explaining that on the first copy you listed the wrong TIN, but that the information provided was accurate otherwise.
If you've got a copy of the one you sent in 2 years ago, attach it for reference as well so that they can update their files and write "Amended" on the top of the initial one.
The cover letter should help them connect the dots that simply "Amended" at the top otherwise might not.