If I change an entry for period prior to my bank reconciliation and replace it with an entry of equal value, will it change the Register Balance for that previous period?

My auditor has looked back at some bank reconciliations and the register balance for that period no longer matches the register balance on my reconciliation report.  Subsequent reconciliations have always balanced, but the register balance does not match on those either at this point in time.  I am having a difficult time trying to determine the entries that caused the balance to change.  I know if I cancel or add a cheque or deposit or journal entry containing a bank entry and date it prior to the reconciliation,  it will change the register  balance.  Or if I void an entry that was created before the reconciliation.  I have on my auditors request last fiscal year, cancelled a couple of cheque entries and replaced them with Journal entries.  If they had already been reconciled, I manually reconciled them, and used the same dates as the original entries.  Could making this type of change in a different time period change the register balance?  To me, it should not matter until year end, but she wants to know the transactions that changed the balances.  I cannot think of a way to do this without doing an audit of every entry to ensure it was not created post reconciliation. We have a lot of entries!  Any ideas on an easy way to trace would be appreciated.