After extensive research, I found the solution to be QIF. Though Quicken states:
Note: QIF import is not available for checking, credit card, savings, 401(k), or any other brokerage accounts.
This appears to be a mis-statement as it's really only enforced when Exporting data. After adding the following four lines (documented [here][1]) to the top of any QIF, I have successfully imported/merged new transactions into an existing Quicken 2012 Checking account. My understanding is this will work for any account, regardless of the type.
!Account
NJoint Brokerage Account
TInvst
^
In my situation I only needed to replace "Joint Brokerage Account" with the account name I wished to import into, even though the type specified is "Invst" and my account is "Checking", this still succeeded.
Quicken QIF Literature: Importing Data Into Quicken (Updated: 4/27/2012 | Article ID: GEN82389) Solution URL: Direct Method