Maybe because the array is just ints?
Shouldn’t I be storing the instances
that are hit, not ints?
You should be storing instances’ indexes - they’re ints. Essentially, if you want to remove a bunch of instances from a HISM by index, you need to remove all indexes in one go, via the Remove Indexes (plural) node. Never in a loop.
You do not need sets - not for what is demonstrated above at least. I use them as the procedural generation in my project is somewhat involved and I need to efficiently operate on a large numbers of elements without worrying about iterating over the same indexes again.
I’ve never used sets before
You probably have, you mastered them somewhere in primary school. It’s usually about fruit, shapes, animals and whatnot:
Since HISMs’ instances always have unique numbers, sets make perfect sense here. If you want to, lets say, drop 3 bombs on the cubes below and remove everything the explosion radius hits, you’d combine 3 sets. Unlike an array, a set of 3 overlapping results would produce the precise number of uniquely indexed elements which you can later on remove with Remove Indexes - all in a single BP execution, and without giving the indexes a chance to reshuffle.