From a comment by user laymonk...
The simple fix involves just cd'ing into the virtualenv, and deleting all the stale links to the upgraded python by running:
find . -type l -delete
(return to home dir)
.. and then re-installing your virtualenv:
mkvirtualenv venv-name
To keep R working in Jupyter after an upgrade: Instructions here.
install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ', 'devtools', 'uuid', 'digest'))
devtools::install_github('IRkernel/IRkernel')