Agree, but you can realign them back in your General Settings which is a hassle.
The bigger issue is what about cases when have multiple fulfillment and multiple invoices to that one sales order (very common in Advance Sales Order). To get numbers unique, maybe DEAR has to think about some setting for the suffix that allows something like this;
SO-2000; (original sales order)
IN-2000 IN-2000-1 IN-2000-2; (3 invoices for 3 part shipped orders)
CN-2000 CN-2000-1 (2 credit notes)
I think Unleashed does something like this.
Coconut Consulting | DEAR Expert Partner