Not always able to take the balance payment with Partial Payments

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Hi, We're experiencing inconsistencies within Shopify when we're taking partial payments. When we go back to the order to take the final payment it won't always allow us. Sometimes you can on the POS system only, and sometimes you can on Shopify only and not the POS. Sometimes you can't take the payment at all and we've had to delete orders and then redo them, even though it says partially paid and only part payment has been taken. Any help with this would be great.