I am having the same problem, but even when I deactivated all of the plugins, the css for my blog was still gone and I can’t edit or download any themes or upgrade a plugin. Deleting the plugin that needs updated didn’t fix the issue either.
It started when I was editing a font size in the the css file and then one of the plugins had an update pop up. After that, when I saved the edited css, all of the content in that file disappeared, and the other themes became uneditable and undownloadable, etc. I do not have the plugin-culprits listed above, and like I mentioned, deactivating all of mine didn’t fix the issue.
