When you want to remove a masternode from the masternode.txt file you have to edit this text file manually.
Make a console session to your server.
Go to the directory with the masternode.txt for this coin. It's easy, we have a shortcut for every project.
Here the example for the Northern coin
Now you are in the correct directory. Edit the text file with vi or nano text editor (vi masternode.txt).
Safe and close the file, that's all. The Phantom daemon will read the new config file automatically.