After completing mechanome quest in Rustbolt, town is changed

So I did a not so long questline that sees me fighting with gnome & mecha gnome leaders to retake the city. After I completed it, towns changed, guards are dead, place is on fire, more than before, and more importantly, Pascal and his bot are gone. Is this supposed to happen, and if so, how can complete a quest I started AFTER this one (cant remember name) with no Pascal or K1N6. Is there something that changes this? Im lost. Oh I returned a month ago after 1 years, so i didnt do A LOT of quests