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for (reverse 0 .. $#a) {
    splice @a, $_, 1 if condition($a[$_]);
}

my (%a, %b);
@a{@a} = ();
@b{@b} = ();
...
# or if order matters,
# @a = grep {exists $a{$_}} @a;
# @b = grep {exists $b{$_}} @b;