Good onenote backup strategy?

Unfortunately, there is no backup option on other OneNote clients than in OneNote 2010/2013/2016 for Windows (and that one is also less than ideal).
There is absolutely no way to backup your notes. The copy that is stored on your Mac is just a temporary cache and absolutely of no use when it comes to restoring your notes. Even when playing back a time machine backup it is not guaranteed that your notes (actually the cache) will get restored.

If your notes are on OneDrive personal (in opposition to OneDrive for Business) there is a totally undocumented (and most likely unintended) trick to get a backup: While you cannot download OneNote notebook "files" (what you see in the browser when logging into OneDrive isn't an actual notebook file but just a placeholder pointing to a hidden file structure) separately, all content DOES get downloaded if that "notebook file" is located inside a (any) folder and you download that complete folder. You can even create a new empty folder on OneDrive (using a browser!) and copy (not move) your notebook "files" you want to back up there. Then download that complete folder. It will result in a ZIP file that holds all notebook content in OneNote's internal file format (folders for notebooks, ONE files for sections).

Now a bad news again: You can not use those files to restore notebooks on a Mac, because OneNote for MacOS cannot handle locally stored notebook files at all. So to restore your notes in case of emergency you ABSOLUTELY need access to a Windows PC with OneNote 2016 from MS Office on it. But this is still better than no backup at all for critical data, right?

Sorry, but as long as Microsoft does not implement a backup system for OneNote notebooks that are stored in the cloud (and no one knows if they are willing to do so), this unofficial way is the only possible method to get a backup at all.

Thanks for the informative (though depressing) reply.

Oouf. That's a really scary situation, where you're putting all your trust into OneDrive and its ability to deal with bad actors. What are the limitations in the Windows backup approach? 

You mean in the backup system that is integrated in OneNote 2016 for Windows?

1. the default settings are nonsense: Just one backup every 2 weeks, on the system drive and an important switch that is needed to save notebooks, that are stored in the cloud at all is not set by default. But all this can be optimized by adjusting the settings.

2. The main drawback: Only notebooks that are currently opened in OneNote are backed up and OneNote must be running for this. So no automatic background backups until these requirements are met.

Microsoft is still insisting on "you don't need a backup because your data is safer on our servers than on your computer". That may be right when it comes to hardware failure fire, flood or theft. But they are not safe from human error, lost connection (subscription / access) to OneDrive or sync problems losing data on the way. So they need to implement some sort of backup. I surely hope they will.

Until then I regularly export my most important notes to PDF (just for a world without OneNote), which is also only possible with OneNote for Windows for now.

Yes, that's what I meant. Again, thanks for info. BTW, the Mac 16.11 version lets you save individual files as PDFs  as well.

If I go to OneDrive in a browser, there's a button to download everything under my Files->Documents. That gives me a zip file with .one files. It's a manual process and I'll lose the versioning data, but I think that plus a Mac filesystem backup is going to work for me.

I get what Microsoft says about OneDrive having a more reliable failsafe than whatever solution an end user could cobble together. I'm sure that's true. Still, we live in strange times, and having a user-controlled backup in addition to your single cloud provider solution for critical data seems like common sense.

Thanks for sharing your considerable knowledge.