You need just one hash. Something like this

my %ids;

my @orig_service_ids = (3,1,4,9,7,12);

# this represents your first while ($sth->fetch) loop
for my $id (@orig_service_ids) {
    $ids{$id} = 1;
    # instead of '1', you could also assign something else as value,
    # e.g. an anonymous array [...], or an anonymous hash {...}, to
    # store associated data, which you could then retrieve later...
}

# ...

my @dest_service_ids = (1,5,8,11,7,2,9);

# this represents your second while ($sth->fetch) loop
for my $id (@dest_service_ids) {
    if (exists $ids{$id}) {
        print "ID $id exists in both origin and destination set\n";

        # ...
    }
}
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