I had a lot of company W-2s returned from SSA for that reason. I transferred all of my W-2s from EasyAcct to Information Return Systems before uploading them to SSA. When uploading from EasyAcct, a W-2 was sent for employees still listed but no earnings. 

BSO has an option for "resubmitting". That is what I used. I hope they don't come back as duplicate files.

When using Information Return System to create electronic files for 1099s, a diagnostic error appeared requiring the e-mail address. It would have been super if that happened when creating the W-2 electronic files.

It sure was a lot of extra work this year.