Removing plugin in Calibre removes it from all instances of Calibre

I had a second calibre portable setup for my Sister and removed the goodreads sync plugin as she'd never use it.

When I went back to my version of calibre it had removed this there also, is this something that can be fixed as whilst not a common occurrence it would be a pain. I've also recently setup a new Calibre instance for Graphic novels so may run into this in future there also.