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I was reading up on this recently, so adding an answer to this old old question.
The npm docs say that by default:
The prefix config defaults to the location where node is installed.
So in your case when you use n to install a copy of node to the default prefix of /usr/local/ it also implicitly changes the prefix for npm to /usr/local/ when that copy of node is running. (i.e. the new node executable is at /usr/local/bin/node)
How to reproduce on Ubuntu 12.04
sudo npm -g install n
sudo npm prefix -g
sudo n 4.1.0
sudo npm prefix -g
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