The save command must be used to store a new generated or modified MIDI file.
During editing modified files are kept in a temporary files folder and will be deleted when closing the application if they were not saved.
Save As ...
The save as command is used to store the file with a new name or to an other folder. It will ask for choosing the new file name and location.
Working folder changes after Save As operation when a new location is selected. For copying files to a slow drive (e.g. floppy disk) better use Windows Explorer than Save As because future operations might access the slow drive and that could slow down the work speed unnecessarily.