Okay, I replayed the mission and I have results, not those I intended or hoped to get, but the ones I got are quite suprising.
First of I removed all other mods, the nude mod, weapon mods, car customisation mod and the Nyte Blade and Cyrus outfit mod.
I loaded a savegame which already had the daedalus and the Thermopylae sitting around the city and I was wearing the Nyte Blade outfit. I suspected that the game would crash while loading, because some files are missing, but suprisingly it did not.
I was capable of selecting the Nyte blade outfit in my wardrobe, change clothes to a different outfit and back, no problem. checked my customised cars which are actually non customisable, no crash, all loaded fine. Then I started the mission Stag film. Intro cutscene did not load and the screen remained black, but after aborting the mission and selecting retry I skipped the cutscene and was straight into the action.
Succeeded in the mission and finished it, cutscene played properly (still wearing the outfit)
and once I got back into the game world, the daedalus was gone. It simply dissappeard and all the changes which where made by modding the sr3_city.lua for the replay mission mod regarding the daedalus where gone. Only the Thermopylae was still sitting safe and sound in the water. All other changes back to vanilla endgame state. My outfit did not dissappear though.
Playing the mission again and then aborting it had the same effect. Daedalus is gone.
Different was, that this time the opening cutscene played flawlessly and the VTOL I flew from the Saints HQ to the mission start did not despawn. I dont know if they despawn in a vanilla game or not though.
Using my Sr3_city.lua had the same effects strangely. Even though the Daedalus is supposed to be there after the Stag Film mission, it was gone. Can someone confirm that? I have a strange feeling its something my savegames affect.
Edit: was using the wrong Sr3_city.lua. Testing with mine actually did something. If I finish the mission the Daedalus and all the changes take effect as the Sr3_city.lua specified. But aborting the mission, removes the Daedalus and all the changes which are specified, even if the changes where in effect already. That means, if I want after endgame changes, I finish the mission, if I want to revert everything back, I abort the mission.