I used do() for illustrative purposes. I would actually recommend using prepare_cached()/execute() instead of prepare()/execute(). do() has to re-prepare the statement, which can take time.

As for your addto_Skip(@row) thing, that's up to you. If you expect to have rows that you cannot insert or update, that would be a useful thing to have.

You can also do something like:

while (my @row = $sth->fetchrow_array )
{
    eval { $sth_insert->execute( @row ) };
    next unless $@;

    eval { $sth_update->execute( @row ) };
    next unless $@;

    addto_Skip( @row );
}
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Though, personally, I would look at using fetch() with bind_columns(), as the best performance option that DBI supports. This is instead of the fetchrow_array().