Bootloader is written for 120MHz, so any program written via the bootloader to MCU must use this frequency value in order to work correctly.

You should use external programmer if you want to achieve any other frequency. 

Connections should be as following: 

TMS - PA13 

TCK - PA14 

TDI - PA15 

TDO - PB3 

TRST - PB4

After using programmer on MINI M4 the bootloader is going to be erased.

In order to enable bootloader on MINI M4 again, you can use programmer to load hex file of the bootloader back to MCU on the MINI M4.