Sales Order Issue - Urgent

I have an issue to resolve.

our user has created a sales order (s1) with 2 materials e.g material1 and material2 for customer c1.

In past another sales order(s2) for material1 of same quantity and for same customer c1 had been created and material had been despatched in august. That sales order was only for material1.

Now what the system did that yesterday when user created a new sales order (s2), system created a sales order and gave the same number as the old sales order had. system simply have added material2 in old sales order and returned its number.

I cannot understand that why system did this. I have advised user to create a new sales order and this time, system has generated a new order number.

Any ideas that why system behaved like this and if i delete item20 which system had added in sales order (s1) instead of creating new sales order then is it OK as despatch advice and invoice for that order had been created in august too??