So as of now having doe the update of terminado as suggested (as well as 
Jupyter, jupyter_core, ipython and tornado)
As well as conda update ipykernel
and:
tom@tomServal:~$ python -m ipykernel install --user
Installed kernelspec python3 in 
/home/tom/.local/share/jupyter/kernels/python3

I still am getting: [E 22:05:30.138 NotebookApp] Uncaught exception GET 
/api/kernelspecs (127.0.0.1)

and no kernels in the menu and hangs when opening a notebook (due to no 
kernels I guess..
So when I attempt to create a new notebook that option is grayed out..

oddly when I run:
tom@tomServal:~$ jupyter kernelspec list
Available kernels:
  clojure    /home/tom/anaconda3/share/jupyter/kernels/clojure
  groovy     /home/tom/anaconda3/share/jupyter/kernels/groovy
  java       /home/tom/anaconda3/share/jupyter/kernels/java
  kotlin     /home/tom/anaconda3/share/jupyter/kernels/kotlin
  python3    /home/tom/anaconda3/share/jupyter/kernels/python3
  scala      /home/tom/anaconda3/share/jupyter/kernels/scala
  sql        /home/tom/anaconda3/share/jupyter/kernels/sql

And my envs are as follows (these were all available in Jupyter before I 
updated to 5.3.1
tom@tomServal:~$ conda info --envs
# conda environments:
#
py27                     /home/tom/anaconda3/envs/py27
py36                     /home/tom/anaconda3/envs/py36
py362                    /home/tom/anaconda3/envs/py362
py36j                    /home/tom/anaconda3/envs/py36j
py36n                    /home/tom/anaconda3/envs/py36n
pyfolioenv               /home/tom/anaconda3/envs/pyfolioenv
tf13rccpu                /home/tom/anaconda3/envs/tf13rccpu
tf3rc                    /home/tom/anaconda3/envs/tf3rc
tf4                      /home/tom/anaconda3/envs/tf4
tf4n                     /home/tom/anaconda3/envs/tf4n
root                  *  /home/tom/anaconda3

As mentioned they are are still visible on the conda tab in the notebook

Given that many if not the majority of jupyter users now use conda this 
seems like an issue..!

I am happy to provide more diagnostic info or accept suggestions as to how 
to fix it? Seems like a missing or misplaced config file of some sort 
(something got moved or is now being pointed to in a new place?)
But At the moment I'm stuck...


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