Yes, you can; and yes, that’s true. Depending on what you are updating, the process can be quite simple. But it can also be impenetrable.
Indeed. These are UUID’s and are not unique to bank accounts. They also appear for customers, suppliers, employees, tax codes, and other things. The simple fact is that batch operations are not for the inexperienced. Nor are they necessary to accomplish any task. Everything they can do can be done by straightforward manual editing.
You should not have expected that to have any effect on overpayments or overdue statuses. That information is unrelated.
Read this Guide for ideas: https://www.manager.io/guides/12951. Based on what you have shown, I think automatic allocation of all your payments will create more problems than it solves. Every one of your overpaid sales invoices is the result of a deliberate allocation of a receipt to that invoice (possibly after an auto-allocation, but always as a result of a deliberate allocation). Overpayment can never be initially caused by auto-allocation. Since you prefer direct allocation anyway, your recovery process will be to View the overpaid invoices and look at the mini-statements at the bottom (a new feature with your update). This will show you exactly which receipts were applied. Then you can allocate those. If everything is truly in balance as you say, when you finish this process you will have no overpaid or overdue invoices.