VOID a Check and Send Another

[TimSchofield]

No you should be using Payments.php

Assuming you initially paid a $100 invoice with a $100 cheque and you allocated the two together.

Now use Payments.php exactly as you did with the $100 cheque but put the amount of -$100 in the amount, and don't select any invoices to pay off against. This voids the first cheque.
Then use Payments.php to and enter the new cheque for $100 and again don't select anything to pay, just leave the payment unallocated.
Now go into supplier allocations and you will see for this supplier a $100 cheque and a -$100 cheque possibly others but forget those). Allocate these off against each other. The supplier account will now show:

Invoice $100
Payment -$100
Void payment $100 (a negative payment will show as a positive in the account listing)
New Payment -$100

Balance $0

Again I think you are over thinking this Paul, the entries are fairly simple

Tim