Yunohost modifications, break the ownCloud internal updater

When I run the updater, on the update screen, the update button appears but when clicked doesn’t do anything, thus breaking upgrades.

I ran through the issue with Lukas Reschke, the security dev for ownCloud/Nextcloud and he determined that it seemed to be an issue with Yunohost’s integration with ownCloud. In the browser console I see a couple of requests for ynhpanel.js which are generating 404’s and some YunoHost SSO cookie stuff.

Now, I’m wondering if there’s any way to turn off YunoHost adding it’s own code when owncloud/update/index.php is called? Even if it’s just something I can temporarily comment out in a file or two…