In Netsuite, you have the option in your Accounting Preferences to turn on "Accept Payment Through Top-Level Customer".
This functionality, in itself, is quite useful and a lot of people use it. It simply means that you can create Invoices in the name of sub customers, but have a Parent Customer make all the Payments. It's a functionality that makes plenty of sense when dealing with subsidiaries, sub-customers or departments or a larger client.
However, it also happens in reality that, for whatever reason, the parent-child link between the entities may be severed. One's instinct would then be to do the same in Netsuite - the system in fact does allow you to simply erase the value in the "Child Of" field on customers, thus liberating it of its parent, and allowing you to post both Invoices and Payments directly to the newly freed child.
You see, Netsuite deals very, very poorly with this situation. In the system, you have Invoices in the name of one entity (the child) and Payments in the name of another entity (the parent). This makes sense as long as the parent-child link exists. Without that link, you've got an invalid situation, from a system point of view.
What happens *exactly* at this point has varied over the last few months. Last winter, we had a customer who separated children and parents. In that case, Netsuite changed the records so that all the Invoices were now Open. The child kept all the debt and the parent kept all the credit. Considering many parent/child relationships had been severed, it took us over 60 hours to correct the data. Then their accountant had to reconcile everything again. Yeah. It was a mess.
More recently, another customer had to sever parent and child again. But this time, Netsuite behaved rather well. The Invoice remained Paid in Full and the Payment was fine. BUT, as soon as you hit the Edit button on the Payment, the invoice being paid instantly vanished. In other words, the Payment record can never, ever be edited again.
The official(ish) word on the matter from Netsuite is that you should NOT be separating parent and child records. Netsuite shouldn't allow you, plain and simple. And I can only assume this will be patched and enforced in the future.
So my recommendation to you is the same: Do Not Separate Parent and Child Records When You Have Invoices Paid By The Parent. Just create a new Customer record and start over, leave the old entities be. Yes, you lose the history. But that is probably better than the chaos you will unleash if you sever the relationship. Anyway, just be careful.