You can also use these overrides to "reset" your config:
Also, have you tried Prodigy logging? Consider using it as verbose as it should give you reference of what prodigy.json you're loading, perhaps seeing where you're loading a config you weren't intending for.
Other users have reported ERRNO 99 issue because they had to restart/end and accidentally didn't realize something else was also running:
Just curious, can you run Prodigy w/o the jupyter-prodigy extension? I want to diagnose if the issue simply Prodigy or the extension.
Like the earlier post, one way to test is to try a different port. This can sometimes be an issue with jupyter-prodigy extension so that's why perhaps you could try a different port with only Prodigy run from a terminal.
Let me know if either of these help or if you're still having issues.