From Jailkit documentation:
Jailkit is a set of utilities to limit user accounts to specific files using chroot() and or specific commands.(...)
So, you did a chroot in your user's shell access..?!
If so, what the surprise..??
Chroot just exist to change the root of directories visible to that user.
But the files still exist there, in the same place, usually. But only visible to the root user.
Regards,
Netino