Other than the obvious, the website going offline, what are the consequences of an ignorant or a malicious user deleting all folders and files while logged in via ssh to his jailkit folders. Is it possible that other sites or server files will be affected. I have no experience in this regard and hope this question doesn't involve an extensive response. Thanks
The idea of the jail is that the user can only break their own web. Make sure that you use PHP-FPM and set it to chroot (best by default).