I think I found a way around this, thanks to starting an old Linux
OpenCPN does indeed create a lock-file in your home directory called "OpenCPN"
you already have a file/folder called "OpenCPN" in your home directory, you get this message. At least on Linux, just click OK and go on, as nothing stops you from running multiple instances of O. Windows is a different story.
So the workaround is to rename your file/folder, called OpenCPN, to something else.
It is a bit strange to use a lock-file called "OpenCPN" in the users $HOME. I'll try to make sure this goes away to the next release, somehow...