I'm having some trouble following your question/spec. See How do I post a question effectively?. I particular, providing input and expected output would probably provide a lot of clarity.

I think you are saying you want to remove already processed elements of the array referenced in $aref_hrefs_inn. You've correctly identified that the element of @$search_array is not linked by lvalue. So, why not use a hash to cache which elements need to go?

my %to_be_deleted;
foreach my $inn_href (@$search_array) {
    if (check_match($args_href) == 1) {
        if ($$flags_href{unique} == 1) {
            $to_be_deleted{$inn_href}++;
        }
        last;
    }
}
@$aref_hrefs_inn = grep !$to_be_deleted{$_}, @$aref_hrefs_inn;
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Code untested, as you've got a lot going on there.