How about this. The script which runs the game renames s:startup-sequence to s:startup-sequence.orig. It then copies a new startup-sequence from the game's directory to s:. This startup-sequence starts off by renaming s:startup-sequence (the one for the game) to startup-sequence.old and then renaming s:startup-sequence.orig to startup-sequence. Then it sets up the assigns or whatever and launches the game. The next time you reboot you will have the original startup-sequence back in place and the game will boot as normal.
I don't actually know if this will work as I don't know whether a script can be renamed while it is running.
--
moto