Now I see that I might have done all wrong : first I use this type of Pro Micro :

as you can see on the PCB it's a Pro Micro but using a bigger PCB- it's wider and uses Mini USB connector.

Then I missed this step compeletly :
http://www.geneb.org/mmjoy2/pro-micro-instructions.pdf

In the end, when I use "Start bootloader" in MMJoy2 and look at the Device Manager on COM ports, I see it reports as "Pro Micro 5V" without any "Arduino Leonardo Bootloader COMXX" device. Yet before I've disconected the EDTracker so that's why COM5 is missing now on the COM port list.