reset/update midi to notation

I am currently evaluating Notation Composer and I am very pleased with interface and intuitiveness. For some reason however, when I play back my score in notation composer, certain parts of the midi are quite different from the notation. This is surely due to my misuse of the application.

My question : Is there a way to select all notes in the score and then generate a new underlying midi which reproduces the raw score. I am mostly interested in transcribing music and obtaining the notation, so I don't need many of the features for modifying the midi. I suspect I somehow manipulated the midi inadvertently, and I can't figure out how to get it to play back the score without modifications.

sincerely,
shelby