zigbee2mqtt cleanup stale devices (nvram / trust center full)

coordinator_backup_remove_stale.sh

#!/usr/bin/env bash
set -euo pipefail

# --- inputs in current directory ---
DB="database.db"                       # Zigbee2MQTT JSONL database
BACKUP="coordinator_backup.json"       # coordinator backup JSON
CLEANED="z2m_coordinator_backup.cleaned.json"
# -----------------------------------

# sanity checks
[[ -f "$DB" ]] || { echo "missing $DB"; exit 1; }
[[ -f "$BACKUP" ]] || { echo "missing $BACKUP"; exit 1; }

# 1) extract IEEE from Z2M DB (lowercase, without 0x)
jq -r 'select(.ieeeAddr!=null) | .ieeeAddr | ascii_downcase | sub("^0x";"")' \
  "$DB" | sort -u > z2m_db_ieee.txt

# 2) extract IEEE from coordinator backup (lowercase, already without 0x)
jq -r '.devices[]? | .ieee_address // empty | ascii_downcase' \
  "$BACKUP" | sort -u > z2m_backup_ieee.txt

# 3) diff lists
comm -23 z2m_backup_ieee.txt z2m_db_ieee.txt > z2m_stale_on_coord.txt
comm -13 z2m_backup_ieee.txt z2m_db_ieee.txt > z2m_missing_in_backup.txt

# 4) build cleaned backup that keeps only devices present in DB
jq --rawfile keep z2m_db_ieee.txt '
  ($keep | split("\n") | map(select(length>0)) | unique) as $keep
  | .devices = (.devices // [] | map(select((.ieee_address // "" | ascii_downcase) as $ieee | ($keep | index($ieee)))))
' "$BACKUP" > "$CLEANED"

# 5) show before/after device counts
before=$(jq '.devices|length' "$BACKUP")
after=$(jq '.devices|length' "$CLEANED")

echo "stale_on_coord:   $(wc -l < z2m_stale_on_coord.txt)"
echo "missing_in_backup:$(wc -l < z2m_missing_in_backup.txt)"
echo "devices before:   $before"
echo "devices after:    $after"
echo "cleaned backup written to: $CLEANED"

coordinator_nvram_reset.sh

#!/usr/bin/env bash
set -euo pipefail

# --- user settings ---
CONTAINER="zigbee2mqtt"                               # docker container name
DEV="/dev/serial/by-id/usb-Silicon_Labs_Sonoff_Zigbee_3.0_USB_Dongle_Plus_0001-if00-port0"  # coordinator serial
DATA_DIR="/apps/zigbee2mqtt/data"                     # Z2M data folder
CLEANED="${DATA_DIR}/coordinator_backup.cleaned.json" # cleaned backup produced earlier
TARGET="${DATA_DIR}/coordinator_backup.json"          # file Z2M restores from
# ----------------------

# sanity checks
[[ -r "$CLEANED" ]] || { echo "cleaned backup not found: $CLEANED"; exit 1; }
[[ -e "$DEV" ]] || { echo "serial device not found: $DEV"; exit 1; }

# stop Z2M so the serial port is free
echo "Stopping container ${CONTAINER} ..."
docker stop "$CONTAINER" >/dev/null

# create throwaway venv for zigpy-znp
VENV="$(mktemp -d)"
python3 -m venv "$VENV"
# shellcheck disable=SC1090
source "$VENV/bin/activate"
pip install --upgrade --quiet pip zigpy-znp

# reset coordinator NVRAM
echo "Resetting NVRAM on ${DEV} ..."
python -m zigpy_znp.tools.nvram_reset "$DEV"

# leave and remove venv
deactivate
rm -rf "$VENV"

# backup current coordinator_backup.json if present
if [[ -f "$TARGET" ]]; then
  cp -a "$TARGET" "${TARGET}.bak.$(date +%Y%m%d-%H%M%S)"
  echo "Existing ${TARGET} backed up"
fi

# place cleaned backup as the restore source
cp -f "$CLEANED" "$TARGET"
echo "Placed cleaned backup at ${TARGET}"

# start Z2M so it restores onto an empty NVRAM
echo "Starting container ${CONTAINER} ..."
docker start "$CONTAINER" >/dev/null

echo "Done"
echo "Watch the Zigbee2MQTT logs for 'Restored network from coordinator_backup.json'"

relates to
Koenkk/zigbee2mqtt#27538
and
Koenkk/zigbee2mqtt#28282 (comment)

I have this issue with mine. How do you use this? I have home assistant on VMware.

I cant help you with VMware.

Write down your Environment to an AI of your Choice and paste the link to this gist too.

Thanks that helped me action it in terminal with AI help ...... but my problem still remains. I am thinking its this one device I have that is the problem.