After reviewing the couple of replies along with the design, it occurred to me that this design is slightly different from the many eval boards available. Specifically, this design implements the VBAT with a Lithium coin cell. As a result whenever, the program (re)starts, the previous value for RTC_FLAG_INITS has been retained and the hardware is working as designed.
I was looking for a software solution, but as is mentioned in several places, whenever the write protection is removed the clock would stop. In this case, stopping for a few instruction cycles would not have a significant effect. However, once the pre-scalers have been set, there is no reason to reload them.
So, to let the system work as intended, the solution is to: Load the new code. Remove all power including the backup cell. Allow the hardware to fully discharge. On power up the software will ‘see’ that the flag is not set and it will initialize with the new values and set the flag. Once that is complete, as long as the coin cell remains in place, the code will not repeat.
The hardware and software are working as intended!