Thank you @RCV. Initially this did not work - I was getting an error message:

"The selected and downloaded transaction amounts don’t match. To continue, resolve the difference."

However, I then noticed that the Bank Deposit was showing the account as my new business checking account, even though the deposit was actually made into a different account. I assume when we changed the settings to make sure that all the new transactions got into the new account, that it maybe changed the past charges as well? Seems odd, but that's the only thing I can think of. When I change the account back to the old account in the bank deposit section, I am then able to match the transactions. 

Do you see any downside to updating these older transactions in that manner? It seems to be the only way that I can match off the transactions, and maybe also resolving a potential issue we didn't know we had with older transactions showing they were deposited into an account that did not exist at the time.