I just cant imagine a vast star empire with such a prolific effect on this particular galaxy just.... dying off. It'd be a long process.
Look at Germany in ww2.. facing against nations twice its size still took years to destroy. I cant imagine a nation like the iscandarians with their advanced magic weaponry just... flopping over.
I can only think of two major ways that empire could fall in a reasonable amount of time.
1, A civil war, which would utterly destroy this part of the galaxy. with how connected the iscandarians are, the entire region would be pulled in and every one would be affected big time.
2, An outside invader of incredible power, like the hau, arrive and open a can for what ever reasons. This however would lead to everyone being affected big time. Likely occupation of everyone or some shit (make for an odd oppression plot but I cant see many aside from myself having a fun time exploring the whole, being oppressed by powers above and trying to overcome.)
I understand you're trying to retcon the iscandarians for your brony race but seeing as your iscandarians are so involved with everyone, it'll be a huge change for them to just fade away.