There's a feature in free Cloudflare accounts called "Speed Brain" that causes WordPress plugins to be deactivated, or the fully deleted from a site on update.
For reasons like this, Cloudflare is not a part of our recommended or supported setup, unless you have paid support for it. For more information see our CDN pagespeed section.
Clients on NerdPress Cloudflare Enterprise and BigScoots Performance plans don't have this feature enabled and won't have this issue.
If you use the free Cloudflare, you'll need to deactivate Speed Brain in your Cloudflare account.
See this tutorial on deactivating Cloudflare Speed Brain from NerdPress.
If you're hosted on BigScoots but without the Performance package, they've acted quickly and done this on your behalf.
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