I tested this in the Demo company and suggest you do so, too, so you can see what's happening.  When you delete an invoice that has already been paid, the invoice shows as Cancel and, although it stays in the list, it doesn't get included in the balance.  The customer balance will reduce by the value of the cancelled invoice and may now even be in credit.  But the tricky thing is that Sage doesn't not alter the receipt from SR so even if you wanted to refund or match it against something else, you can't. Instead, select that SR and choose Unallocate, which sets it back to SA.  You can then re-input your sales invoice and match it against the SA.

Thank you so much Anita. I had eventually arrived at much the same conclusion and did unallocate the SR, re-inputted the SI and matched the two. The weird thing is that I still have a o/s balance from the original SI in the customer account. That suggests that I've done something else wrong (or misunderstood my own error). Guess I have some more thinkinf still to do...

Thank you for your help :)