The solution I found is to create a side profile, even if it doesn't show up it will be created, open Opera on the new profile and go to about to find out which number refers to that instance of Opera, just to be able to delete all the instances we don't want to use.
Then since I had already a Virtual Machine with windows 10 I went and downloaded Opera there and created side profiles with the Icon colors I wanted, copied them to my host machine.
After that I went into the taskbar folder of Windows and modified the properties for the Opera Instance without an icon and selected the previously copied Icon for my Virtual Machine.
Apart for the fact that the main instance of Opera still doesn't show the instances, it's working perfectly, seems like nothing ever broke lol.