Well a loss of control of your own data on someone else's service isn't a feature and should be something you should be expecting (create backups of your own data more often), yet as soon as everyone takes the 'free' upgrade bait on a third-party service, then 'all bets are off' including Github.
Seriously for organizations, you're better of in self-hosting your own projects on-premise with open-source alternatives like GitLab (recommended), cgit or even Gerrit to avoid nonsense like 'centralising everything to GitHub' in the long term. [0]
Seriously, you should store wiki pages as .md files in a /wiki folder in your repo, regardless of your git repo hosting provider. I'm positive wiki pages are stored in a separate git repo alongside your code, anyway.
The more that lives in the codebase itself, the better -- ideally this would not only include wiki pages, but also issues, comments, PR threads, etc.
Github treats wikis as another git repository. I regularly use this to backup the wikis I have on github.
If your project is named `username/repository` then your wiki can be cloned at `git clone git@github.com:username/repository.wiki.git`.
This approach is something I never quite figured out. What is the point of documenting your project in another repository? Based on what OP just explained this is one of the only explanations I can come up with (GitHub treats this as an extra that you must pay for).
i like this advice