Problems upgrading -current with pkgbase

[Andreas Nilsson]

Hello,

I'm trying to upgrade my -current with pkgbase, using boot environments:
$ bectl list
BE           Active Mountpoint Space Created
13C-20190902 NR     /          72.3G 2019-09-02 13:43
13C-20190916 -      /tmp/be_mount.JZ2z         127M  2019-09-18 11:21

Trying to go from a checkout 20190902 to 20190916, and it seems there have
been some reorganization as how packages are created, quite a few smaller
utilities like

FreeBSD-libutil-13.0.s20190902093212
FreeBSD-libcom_err-13.0.s20190902093212
FreeBSD-libz-13.0.s20190902093212

seems to have been merged into
FreeBSD-utilities: 13.0.s20190916114708

However, after upgrading all packages and installing FreeBSD-runtime, I
notice that my /etc/passwd is reset to what is found on a new install.

How to go about doing this upgrade without having important files reset to
"factory default"?

Best regards
Andreas