How do I get the plugins back??

Hey, something seriously strange just happend here. First, all plugins were gone. Meaning, they was still installed when checking bu FTP, but the dashboard said "you have no plugins installed". We restored the site from a backup point, and got most back. But still, some plugins is just missing. They are not showing in the admin dashboard even they clearly is installed, and the WPMUDEV dashboard also says "installed". I guess the solution is to uninstall by FTP and then reinstall, but for future use, do you have any idea of what may have caused this? ( We have not installed anything new or made any changes)