[Bug 201745] The disk changes are automatically partially reverted after the system rebooted

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=201745

            Bug ID: 201745
           Summary: The disk changes are automatically partially reverted
                    after the system rebooted
           Product: Base System
           Version: 10.1-RELEASE
          Hardware: arm64
                OS: Any
            Status: New
          Severity: Affects Many People
          Priority: ---
         Component: kern
          Assignee: freebsd-bugs at FreeBSD.org
          Reporter: mom040267 at gmail.com

Parts of my 10.1.2 system keep disappearing after reboot. When I change
something on the disk (a file, or I install a port), it works fine - up until
next reboot. After the reboot, with a very good chance, my changes are gone.
For example, I just installed several ports, but after the reboot they all
disappeared:

Jul 21 02:02:32 corvin pkg-static: wireshark-1.12.6 installed
Jul 21 02:18:48 corvin pkg-static: m17n-db-1.6.5 installed
Jul 21 02:19:03 corvin pkg-static: libotf-0.9.13_2 installed
Jul 21 02:19:22 corvin pkg-static: m17n-lib-1.6.4_6 installed
Jul 21 02:21:11 corvin pkg-static: emacs24-24.5,3 installed
Jul 21 02:27:49 corvin devd: check_clients:  dropping disconnected client
Jul 21 02:35:54 corvin anacron[1280]: Job `autoupdate' terminated
Jul 21 02:35:54 corvin anacron[1280]: Normal exit (1 jobs run)
Jul 21 08:20:16 corvin reboot: rebooted by oleg
Jul 21 08:20:16 corvin pulseaudio[1567]: [(null)] module-x11-publish.c:
PulseAudio information vanished from X11!
Jul 21 08:20:16 corvin syslogd: exiting on signal 15
Jul 21 08:20:34 corvin syslogd: kernel boot file is /boot/kernel/kernel
Jul 21 08:20:34 corvin kernel: Copyright (c) 1992-2014 The FreeBSD Project.
Jul 21 08:20:34 corvin kernel: Copyright (c) 1979, 1980, 1983, 1986, 1988,
1989, 1991, 1992, 1993, 1994
Jul 21 08:20:34 corvin kernel: The Regents of the University of California. All
rights reserved.
Jul 21 08:20:34 corvin kernel: FreeBSD is a registered trademark of The FreeBSD
Foundation.
Jul 21 08:20:34 corvin kernel: FreeBSD 10.1-RELEASE-p23 #0: Thu May 14 13:35:13
UTC 2015
Jul 21 08:20:34 corvin kernel:
root at amd64-builder.pcbsd.org:/usr/obj/usr/src/sys/GENERIC amd64
Jul 21 08:20:34 corvin kernel: FreeBSD clang version 3.4.1
(tags/RELEASE_34/dot1-final 208032) 20140512
Jul 21 08:20:34 corvin kernel: VT: running with driver "vga".
Jul 21 08:20:34 corvin kernel: CPU: Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
(3392.35-MHz K8-class CPU)
Jul 21 08:20:34 corvin kernel: Origin = "GenuineIntel"  Id = 0x306c3  Family =
0x6  Model = 0x3c  Stepping = 3
Jul 21 08:20:34 corvin kernel:
Features=0x178bfbff<FPU,VME,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,PSE36,CLFLUSH,MMX,FXSR,SSE,SSE2,HTT>
Jul 21 08:20:34 corvin kernel: Features2=0x201<SSE3,SSSE3>
Jul 21 08:20:34 corvin kernel: AMD Features=0x28100800<SYSCALL,NX,RDTSCP,LM>
Jul 21 08:20:34 corvin kernel: AMD Features2=0x1<LAHF>
Jul 21 08:20:34 corvin kernel: TSC: P-state invariant
Jul 21 08:20:34 corvin kernel: real memory  = 2147418112 (2047 MB)
Jul 21 08:20:34 corvin kernel: avail memory = 2045800448 (1951 MB)
Jul 21 08:20:34 corvin kernel: Event timer "LAPIC" quality 400
Jul 21 08:20:34 corvin kernel: ACPI APIC Table: <VBOX   VBOXAPIC>
Jul 21 08:20:34 corvin kernel: FreeBSD/SMP: Multiprocessor System Detected: 2
CPUs
Jul 21 08:20:34 corvin kernel: FreeBSD/SMP: 1 package(s) x 2 core(s)
Jul 21 08:20:34 corvin kernel: cpu0 (BSP): APIC ID:  0
Jul 21 08:20:34 corvin kernel: cpu1 (AP): APIC ID:  1

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