"There are # physical volumes missing" - error in pvscan even when the PVs are present

The Problem

The output of pvscan command shows ‘There are # physical volumes missing’, but these physical volumes indeed exist and work well.

# pvscan -v -d
  WARNING: lvmetad is running but disabled. Restart lvmetad before enabling it!
  Using physical volume(s) on command line.
  Wiping cache of LVM-capable devices
  Wiping internal VG cache
  There are 3 physical volumes missing.  <<----
  WARNING: Device mismatch detected for VGExaDb/LVDbSys1 which is accessing /dev/xvda2, /dev/xvde1 instead of (null).
  WARNING: Device mismatch detected for VGExaDb/LVDbSys2 which is accessing /dev/xvdd1, /dev/xvde1 instead of (null).
  WARNING: Device mismatch detected for VGExaDb/LVDbOra1 which is accessing /dev/xvdd1 instead of (null).
  WARNING: Device mismatch detected for VGExaDb/LVDbSwap1 which is accessing /dev/xvdd1 instead of (null).
  WARNING: Device mismatch detected for VGExaDb/LVDoNotRemoveOrUse which is accessing /dev/xvdd1 instead of (null).
  WARNING: Device mismatch detected for VGExaDb/LVDbVdR2D201VM04DBFSC4 which is accessing /dev/xvda2 instead of (null).
  There are 3 physical volumes missing.  <<----
  PV /dev/xvda2 VG VGExaDb lvm2 [24.50 GiB / 0 free] <<---- exists
  PV /dev/xvdd1 VG VGExaDb lvm2 [62.00 GiB / 0 free] <<---- exists
  PV /dev/xvde1 VG VGExaDb lvm2 [96.00 GiB / 23.36 GiB free] <<---- exists
  PV /dev/xvdf VG VGExaDb lvm2 [150.00 GiB / 20.00 GiB free]
  Total: 4 [332.48 GiB] / in use: 4 [332.48 GiB] / in no VG: 0 [0 ]

# ls /dev/xvd*
... /dev/xvda2 ... /dev/xvdd1 ... /dev/xvde1 /dev/xvdf ...

The Solution

The ‘flags’ parameter is wrongly shown as ‘MISSING’ for the three PVs in file: /etc/lvm/backup/VGExaDb

--snippet--

physical_volumes {

 pv0 {
  ...
  device = "/dev/xvda2" # Hint only

  status = ["ALLOCATABLE"]
  flags = ["MISSING"] <<----
  ...
 }

 pv1 {
  ...
  device = "/dev/xvdd1" # Hint only

  status = ["ALLOCATABLE"]
  flags = ["MISSING"] <<----
  ...
 }

 pv2 {
  ...
  device = "/dev/xvde1" # Hint only

  status = ["ALLOCATABLE"]
  flags = ["MISSING"] <<----
  ...
 }

pv3 {
  ...
  device = "/dev/xvdf" # Hint only

  status = ["ALLOCATABLE"]
  flags = []
  ...
 }
}

Follow the stpes outlined below in order to resolve the issue:

1. Schedule a downtime window to boot the server under rescue mode.

2. Backup the file ‘/etc/lvm/backup/VGExaDb’:

# vgcfgbackup -f VGExaDb.old -v VGExaDb

3. Change the following parameter for pv0/ pv1/ pv2 in file ‘/etc/lvm/backup/VGExaDb.old’

From:

flags = ["MISSING"]

To:

flags = []

4. Execute the commands below

# vgcfgrestore -f VGExaDb.old -v VGExaDb
# vgchange -a y VGExaDb

5. Reboot the server:

# shutdown -r now