Can I re-install MacPorts but leave my Python installation, done via MacPorts, alone? Okay, I admit it, I didn't really think it through when I clicked on the button to upgrade to Sierra. Having done that, I've of course made MacPorts lose its mind. I mostly don't notice because once I install Python and PIP, I don't do much with MacPorts -- except to install things like LaTeX or wget. 

Can I re-install MacPorts without messing up my Python installation? I have a lot of packages installed -- numpy, scipy, nltk, sklearn, etc. -- that I would just as soon leave alone. Everything is working well.
The answer is unknown.

Macports is only supported and tested if you do a complete reinstall of it when you chnage the versions of macOS used.

You might be get away with rebuilding only a few of the ports but if you have a problem the only support is delete and reinstall as no one has the time to see what happens when you chnage the OS.