First, as an FYI you don't really need the 'Open File...' step; simply calling the "Perform Script..." in the external file will cause it to open the file. It won't hurt anything to use it, it's just not required.
Second, the layout that is active: when your script in the Parent file runs and opens the 'Office' file, it runs the 'Startup' script in 'Office', yes...but then it returns to the 'Parent' file and the calling script, and exits that script. You might simply need a 'Select Window' step to reactivate the window from the 'Office' file.
Third, do you have any scripts defined for the 'OnFirstWindowOpen' script trigger in the 'Office' file? Those triggers will also be running when you open that file.
Lastly, you are correct - the path is NOT stored in the script step. The path to the 'Office' file is stored in the 'External Data sources' of the 'Parent' file. If the path defined there to the 'Office' file isn't correct, it will ask you to find the file being referenced. You actually should get that dialog any time you try to access something from Office: a layout with fields from it, the Manage Database window, etc.