Reconcile a batched electronic payment in bank feed

HI community members, 

I am writing to seek some guidance on matching and reconciling a batched eletronic payment showing in bank feed. 

Long story short, we follow the steps below to pay bills:

1.Pay bills

2. Electronic Payment

3. ABA file and upload to internet banking to make the payment 

Once the payment is made, the total will then show up in the bank feed for reconciliation. We then click match transactions, the corresponding eletronic payment amount will appear as a transaction to match with the bank feed. However, this won't happen when somebody removes any transactions when uploading to the bank. For example: Eletronic payment prepared in MYOB for 6 invoices totalling $1000 for different suppliers, when my manager uploaded to internet banking, she removed 1 invoice from the ABA file which is $50 resulting the actual payment went out from the bank only $950 and this is what shows up in the bank feed now. I tried to use that match function, nothing appears because in MYOB, that particular eletronic payment file is $1000 where the actual payment in bank feed is now $950. Please advise how do I reconcile $950 sitting in bank feed, which account should I code it to? Many Thanks