you can vi the file and delete the unwanted lines and save then copy it back into the mail directory.
It won't mess up the mail (elm) program.
Your mail program reads/creates a plain text file, there is no special formatting, except for the header info that it creates for each email.
You won't screw up the program by editing the file that contains your emails.
But you can try to delete complete messages, try not to leave a partial messages.