I wish this was true. My workflow from back in the early days of node has always been to `npm install` external dependencies, then `npm link` (symlink) the dependencies I'm working on. But npm >= v5 removes such symlinks if I `npm install` anything afterwards. I spend a significant amount of my time re-linking what npm install unlinked.
Usually when I hit a problem like this it's because I'm things have moved on and I'm doing something wrong. But when an npm developer says "consider npm as it is to be broken" and closes the issue [1], I'm not so sure.
[1] https://github.com/npm/npm/issues/17287#issuecomment-4008339...