I'm newbie, so if understand correctly I've done the 2 option ("lots of modules, each of which you've used npm link to install and you want to remove one of those").
To better explain, I've followed the creting node tutorial, so I've created some folders each one having 3 files:
One .html
One .json
One .js
After that I've used npm link for each of these. But now, I want to remove just one of them.
Could this be caused by the fact that recent versions of npm may without warning remove nodes that are not included in package.json? So the npm remove command is removing one node, but then npm is removing the rest because they have not been included in the package?