1) Download the latest installation files -- select “Version 4.x”, then “1. Installation_4_x” and finally “USBDM_4_x_Win.msi”. Run the installer.
2) Connect the USBDM to a USB port, but make sure it isn't connected to any target board.
3) Start the Bootloader.exe (as of version 4.9 its entry in the Start menu is called USBDM Firmware Updater which is a better description).

To flash a non-standard firmware such as the one that enables the serial port on the original USBDM (without ARM and Kinetis support) uncheck the option "Auto update BDM firmware", then click on "Load Source File" and locate S19 file with the modified USBDM_JMxx_CLD with Serial Port enabled. (Naturally this only makes sense if the Rx and Tx pins on the USBDM hardware are brought out and can be connected to the targt).
For standard hardware, the correct flashimage will be automatically loaded.

Finally click on "Program Flash".

Download the modified S19 file with serial port function enabled: USBDM_JMxxCLD_V4_withSerial 4.9 .