As I know, all ships that presented in the 'previous mission' will act in the 'next mission', if it is named on the same name.
Unextract the last two missions(Clash of the Titans II and Apocalypse, and see those events, and ship properties.
I am using this 'Red Alert Carry Status' in my campaign in a case of an orion, but I haven't tested if the missions are in a campaign(I am at mission 23 and there would be 35, and until the remaining 12 are not done, I don't make the campaign file.)
... Just saw your location, a HUNGARIAN?
Ha az vagy, akkor már ketten vagyunk!