Razing all the buildings in a captured town isn't really a negative, you already lose most of them, you just build them up one after the other until you get back to the city limit. It doesn't cost anything, just takes a few more turns. I'm not suggesting reducing the city to level 1. I'd also personally like a pop-up when you capture a city offering you the choice to keep the current race or convert it to your own, destroying all the buildings when capturing it would make this possible.
Also we are talking about soldiers, fighting in multiple wars, those silver weapons or nevril armors likely wont last very long without repairs or replacement and without the production building that can't happen right? So it makes perfect sense to me that they'd lose the perks. Likewise based on the amount of construction going on these wars take place over many years and your squads are probably getting fresh blood every once in a while, so it would make sense that buildings to train these recruits still exist somewhere in your empire otherwise they'd get inferior field training and the squad as a whole would take a penalty.
Also we are talking about soldiers, fighting in multiple wars, those silver weapons or nevril armors likely wont last very long without repairs or replacement and without the production building that can't happen right? So it makes perfect sense to me that they'd lose the perks. Likewise based on the amount of construction going on these wars take place over many years and your squads are probably getting fresh blood every once in a while, so it would make sense that buildings to train these recruits still exist somewhere in your empire otherwise they'd get inferior field training and the squad as a whole would take a penalty.