As others already pointed out splice is the way to go, since delete only shrinks the array if the element you're deleting is at the end of the array. But the former is more costly. So, depending on you actual code/application, suppose that you may have to eliminate a few elements at a time: you may use the latter and "empty the trash can" later:

delete @array[bad_indices()];
@array = grep defined, @array;
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Of course this assumes that you do not want want undefined elements in your array, which seems to be the case, from the description you give.