My first thought on this matter, is that if the balance is off by a certain amount, one or more missing transaction should add (withdrawl or deposit) to the missing amount.
The software I am using for this uses an SQL Backend (Money Manager Ex) which makes it easy to query for missing / duplicate transactions.
The qfx file, from my bank, can be converted into a csv file and be filtered, using excel or anything else that can read that file format.
The csv file also has unique values for each transaction, and this is useful to find out if a transaction has accidently been imported twice provided it is also imported.
So how does one tell if they need to look at the csv or the MMEX transactions, the withdrawls or the transfers or the deposits, to find out what is missing?
It seems to me that after that, looking for only the withdrawl transactions that are less than or equal to the missing balance would be a good place to start, and then trying to find how a combination of this add up to the missing balance might shed some light on it; or...one could left join the unique id's to find the missing transactions in either using the same date range for both data sets MMEX and csv.
I already know how to look for duplicates.