I had a similar issue, I installed a private library and I could not use the cluster in a notebook for any commands.

I fixed it cloning the cluster, it was like the cluster was saturated. The error I got was something like this:

Failure starting repl. Try detaching and re-attaching the notebook.

Other alternative is to install the new libraries in the notebook instead of using an init_script in the first cells.

Hope it works!