I don’t think it matters either way. As you said, when you set up an an arrangement you’re just giving the customer a reference against which to pay, and presumably then your internal processes allocate the payment where you want it.
All of the original individual invoices have been issued previously and hopefully if you had to use the county court to enforce you would be able to produce separate records supporting each debt, so the customer should be well enough aware of how the total debt is added up. If not, they can always ask.
I suppose it might make things a little clearer for them if you gave all the invoice numbers when terminating the payment arrangement, but I can’t see it affecting your ability to recover.
