Yes, GetSummary won't work. Summaries are calculations that operate on a given found set, so they cannot be used to establish a found set in the first place.
You need to use aggregate functions, Sum() in your case. Assuming there's a relationship between invoices and orders, you could add a calculation to invoices like:
5 < Abs( Sum( Invoice Line::Total ) - Sum( Order Line::Total ) )
Or, actually, I suspect you already have the fields that calculate invoice and purchase order totals, so you can reuse them:
5 < Abs( Invoice::Total - Order::Total )
This will evaluate to 1 (True) when the discrepancy is more than $5 and to 0 (False) otherwise. Search by this field you'll get the invoices you need.