All is not yet lost. First, check out the argument between Ca5(PO4)3OH and chee68 under the "LOR limits" post. Some programs may have downloaded your application. Literally, this means that they can view your application from a computer but they may not have already printed a hard copy for your file. So some programs may have already printed a hard copy and placed it in your file. Despite that there a 2 things that you can do.
1. deassign the General Surgery LOR and assign a different LOR. Programs that have not printed a hard copy will not have any record of that LOR once the LOR has been deassigned. Programs that have a hard copy for your file will always have a record though. 2. ask that LOR writer to write another LOR for ORTHO not GS and then use the new LOR. This may be a good idea especially if you're sure he had initially written a very strong LOR and will write another very strong revision.
It's difficult to know the extent of damage if any from the GS LOR. Deassign it asap to limit any damage.
Just out of curiosity, I am trying to imagine how he could have written a GS LOR. Where do you think the miscommunication happened?

Do not fret, this happens all the time and does not in any way affect your application. Program directors realize that the attendings can be inaccurate in many different areas - we've had recommendation letters that refer to the wrong student in the body of the letter!

Bottom line - if you suspect it is a strong letter - use it.

William N. Levine, MD
Vice Chairman, Education
Residency Director
Columbia University Medical Center
New York, NY