So I had an issue with my AVR ISP programmer. I probably killed one of my ATTiny84, and MKII stopped working (PC didn't registered connecting programmer into USB). Reversed LED polarity on output pin or oscilloscope was probably the cause. I changed XTAL (unnecessarily) for new one on the programmer (because i heard "click" sound after disconnecting from USB), I thought only "mechanical" part that could make this sound and may be broken was XTAL so i changed it, but it didn't fixed anything (duh).
Then I tried reupload firmware, and that fixed part of the issue. Programmer now works, but only in Atmel Studio. Before this issue I had in Arduino IDE Tools>Port COM1 and COM4 and COM4 was always my connected programmer. Now I am able to programm MCUs via Atmel Studio, but I can't see COM4 in arduino. Could there be any issue with programmer?
I also tried reinstall AVR ISP drivers and install libusb0 again...
The AVRISP mkII is a pure USB device. It doesn't create a serial port, thus it no shoing up in the Tools > Port menu is normal and expected.
The problem is likely that the driver used for the AVRISP mkII is incompatible with the AVRDUDE tool the Arduino IDE uses. The solution is to install the correct driver:
I know, that is what I meant by "I also tried reinstall AVR ISP drivers and install libusb0 again..." using Zadig (I tried libusb-win32 and libusbK). A have already done that. And I maybe didn't mention it before but I actually had this programmer in Port list before this issue.
All I know is that I've been using a genuine Atmel AVRISP mkII for 8 years and it never has a port. However, I just looked at the link you posted and I now see that you're not using an bAtmel AVRISP mkII, so I'm not able to help you.
I can only advise you to replace your non-working programmer with one of the USBasp programmers the Chinese sellers sell on eBay. Even though I paid full price for the Atmel AVRISP mkII, I never use it because I prefer my cheap clone USBasps.