Hi linleyscott,
To clarify, are you referring to a transfer transaction from one bank account to another?
As a general rule of thumb, the bank reconciliation will only get affected if the transactions in the bank account do not match the transactions in your QuickBooks company. As long as the money movement is reflected in the bank account and you ensure that you have that money movement/transfer recorded in QuickBooks, the bank account will reconcile.
Bonny