Due to changing schools before junior year, I have been unable to continue any of my EC’s for more than two years. Since my old school was outside the US, the activities available were really different than my current school. Even so, I feel as though I have some pretty unique and somewhat strong EC’s, but they’re split in half between what I did my freshman/sophomore years and my junior/senior years. Would this work against me when applying to some top schools?
No
No colleges will understand your circumstances.
It really doesn’t matter whether they count it for you or against you. There is nothing you can do about it but to lay your case out as well as you can and make sure that you have at least one safety.