There's a way to do this, and it's not ERAS who will get confused.
Okay, so let's say John Smith, MD is writing you a letter for both Internal Medicine and for General Surgery.
On ERAS, you make one listing which says, Med-John Smith, MD, and another which says Surg-John Smith, MD, or some variation on that.
Those titles are just for you to know which letter it which, but more importantly, for the ERAS person at your school to know how to connect the actual letter with the ERAS name. (That's the person you need to make sure ISN'T confused about what you're doing). Just talk to him or her, tell them what to expect and what the abbreviations mean, and you should be okay.
Does that make sense?