The function save_next_reference defined in includes/db/references_db.inc just saves the given reference to the table without any increment using:
function save_next_reference($type, $reference)
$sql = "UPDATE ".TB_PREF."sys_types SET next_reference=" . db_escape(trim($reference))
. " WHERE type_id = ".db_escape($type);
db_query($sql, "The next transaction ref for $type could not be updated");
The above function is called from admin/forms_setup.php to post the form variables just as is into the sys_types table.
The file includes/references.inc has defined the (class references) methods save() and restore_last() which first increment or decrement and then call the above function.
Hence in the file @kvvaradha referred to - manufacturing/includes/db/work_orders_db.inc - the save() method does not need any increment in the argument.
Furthermore, the import_transactions extension has a redundant line 250 in modules/import_transactions/import_transactions.php
Hence nothing needs to be done in the FA codebase for now.