recently added users and synced files are removed from the (web)client after reboot of the Pi but still available in the data dir. There are no errors inside the logs and I don`t know how to trace down the problem.
I am using a raspberry Pi 3, raspbian stretch April 2018, Nextcloud 13.0.0, Apache 2.4.25, PHP: 7.0.27, mysql Ver 15.1 Distrib 10.1.23-MariaDB
It could be a similar issue, as it sounds like you have an external hard disk drive and maybe another drive for the database. And the one for the database could be broken resulting in the “reset” in the web client, while the data is still existing in the data directory (on the hard disk drive?).