I think that the bit you need to change is in Build.pm. If you look for sub build_changed_flags you should find this piece of code:
$cond = GT::SQL::Condition->new (
'isChanged', '=', 'No',
'Mod_Date', '>=', $date,
'Add_Date', '<', $date
);
I think that the line in red says ignore links which are new. If you delete it you should be able to flag new links as changed.