I am sorry to hear you are having trouble using your Zumo 32U4.
For each Zumo 32U4 or other device based on the Pololu A-Star 32U4 that is connected to your computer, you should only see one COM port in the Device Manager. If you are seeing multiple A-Star 32U4 COM ports for the same device, it seems like there might be a problem with your computer or its USB drivers that is preventing it from properly detecting when a USB device is removed.
What USB devices do you have connected to your computer? Are they connected directly to the computer, or are you connecting any of them through a USB hub? What version of Windows are you using? In the Device Manager, please open the “View” menu and select “Devices by Connection”, and then find your COM port devices. Please take some screenshots and post them here so we can try to better understand what is going on. If you have another computer available, please try programming the Zumo 32U4 from that computer.