there is no need to panic. you are just submitting the common application form tomorrow, not necessarily all of your LORs. Those can be sent to the programs as they are submitted by your letter writers(as long as this is before the individual program deadlines). if i were you, i would not submit the medicine letter because once submitted, the program can print it out and put it in your file. even if you switch it out at a later date, this won't automatically mean that they won't see it. as long as your other letters roll in over the next four to six weeks, i dont see this as a problem, but that's just my opinion
