Deleted SO Shipping Data Entry showing up in SO Invoice Data Entry with 0 cost

Currently, we're on Sage 100C 2017 v 5.4, this was a recent upgrade from v 4.9 last September.

One of our user is noticing that deleted orders in the SO Shipping Data Entry batch is showing up in the SO Invoice Data Entry batch that is billing to the customer with 0 cost on the invoice but it does not print the invoice. When you click on the invoice a message saying "Unable to Create invoices for this batch. Batch created in Shipping Data Entry" pops up.

In the previous version, a deleted order in the SO Shipping Data Entry batch will not show up in the SO Invoice Data Entry batch and a user can use the deleted invoice number instantly without having to wait for the batch to update but now the invoice will show up in the AR Invoice History file as well.

Is there a setting that I can change or is this something new in the new Sage?

Any insight will be greatly appreciated.