Hi Floodie,
in the FIRST measure of a MIDI file there are stored the so called "Setup Data" (e. g. Tempo, Time Signature, Channel Voices, Channel Volumes, Effect Settings and much more).
When you press "Execute", this first measure will be rewritten. At this time, the modified MIDI file exists only in the Random Accesss Memory (RAM). Therefore, the file still has to be SAVED as a (new) FILE, finally.
Important: Before pressing "Execute", first press "Song STOP" button (not Pause!) to set the MIDI file "to the beginning".
Best regards,
Chris