Well while it's a good idea, the problem is the max number of levels per episode is 32. Since Duke has more levels than that, you can't do the whole game in one episode. Otherwise the only other thing you have to change is the episode end code for when you beat the final bosses. The Line "endofgame 52" is in the dying state for every boss in the game, so if you change that to something that advances the level number instead you would be good to go.
setvarvar TEMP VOLUME
addvar TEMP 1
setuserdef[].level_number TEMP
I tried this as a replacement for "endofgame 52", it didn't work but, this is the kinda thing you need. If you can't get that to work you could replace "endofgame 52" with spawn ACCESSCARD, to have the boss drop a blue key card upon death. Then you could add a nuke button behind a key card door in the boss maps. Hope this is helpful.
Dukeis1
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