Can someone clarify this for me…QBO Advanced

We run VAT on a Cash Basis

We are filing the VAT return for November and December. 

A September dated customer invoice was paid in November and discounted.  It is showing on both the Exception Report and also in the Sales VAT report (ie twice).  Is this an error?

I contacted QBO support and they said it’s because it’s a filed transaction (which it isn’t) and wanted to talk me through undoing the Sep/Oct Return?  Surely this isn’t correct?

Any help would be appreciated as I am in doubt.

Many thanks