Bank Reconciliation... how to move on?

Hi, 

Briefly, about myself:

-I use Quick book desktop premier non-profit version.

-I have not completed bank reconciliation for June and July. 

-I am temporary person who is taking over the role until new accountant is hired. 

I have a discrepancy in bank reconciliation for June and I know the cause of it: (1) Somebody is trying to re-deposit cheque and (2) other cheque is simply a fraud as the cheque number is way too huge to be ours ... one digit more than where our company is at. Basically, there are 2 extra deposits than expected. We already asked the bank for investigation. 

I want to move on to the next month's bank reconciliation but since the balance does not match, I cannot complete the bank reconciliation for June yet. I noticed that the former accountant made a liability account (2000's) for transactions that needs to be hold temporarily until they have been investigated. From her past journal entries, I figured out how to write these fraud/duplicate cheques in general journal. But again, the issue that I have is that I cannot move onto July's statement until June's balance matches. In order to make the balance match, I thought of changing the initial balance (ie. add the amount of duplicate and fraud to the initial balance) so the amount in QB and bank statement would match. However, I am not sure if this is the right way to go. I do not know if this info would help but I do not think she forced QB to reconcile as I cannot find any record in "reconciliation discrepancy" account. How should I go about?

Thank you so much.