diff --git a/scripts/retire-unused-apps.sh b/scripts/retire-unused-apps.sh
index 269cff6092..a7af8440f0 100755
--- a/scripts/retire-unused-apps.sh
+++ b/scripts/retire-unused-apps.sh
@@ -47,6 +47,12 @@ kubectl_bin="${KUBECTL:-kubectl}"
 poll_seconds="${RETIREMENT_POLL_SECONDS:-10}"
 poll_attempts="${RETIREMENT_POLL_ATTEMPTS:-90}"
 readonly kubectl_bin poll_seconds poll_attempts
+# A layer retrying an unrelated failing health check passes through a
+# Progressing phase every retry interval, so its state is sampled until it
+# settles rather than judged at one instant.
+settle_seconds="${RETIREMENT_SETTLE_SECONDS:-15}"
+settle_attempts="${RETIREMENT_SETTLE_ATTEMPTS:-40}"
+readonly settle_seconds settle_attempts
 readonly releases=(crossview/crossview headlamp/headlamp)
 readonly clusters=(backstage/backstage-db)
 readonly namespaces=(crossview headlamp backstage)
@@ -140,15 +146,21 @@ command -v jq >/dev/null || unknown 'jq is required'
 #    this retirement. Any other not-Ready reason, such as a failed build or
 #    apply, leaves the inventory unproven and is refused.
 for layer in infrastructure-controllers infrastructure apps; do
-  kustomization="$(k -n flux-system get kustomization "${layer}" -o json)" ||
-    unknown "cannot read the ${layer} Kustomization"
-  jq -e '
-    (.status.conditions // [] | any(.type == "Ready" and
-      (.status == "True" or (.status == "False" and .reason == "HealthCheckFailed")))) and
-    .status.observedGeneration == .metadata.generation and
-    (.status.inventory.entries | type == "array" and length > 0)
-  ' <<<"${kustomization}" >/dev/null ||
-    fail "the ${layer} Kustomization has not applied its current generation with a non-empty inventory"
+  attempt=0
+  while :; do
+    kustomization="$(k -n flux-system get kustomization "${layer}" -o json)" ||
+      unknown "cannot read the ${layer} Kustomization"
+    jq -e '
+      (.status.conditions // [] | any(.type == "Ready" and
+        (.status == "True" or (.status == "False" and .reason == "HealthCheckFailed")))) and
+      .status.observedGeneration == .metadata.generation and
+      (.status.inventory.entries | type == "array" and length > 0)
+    ' <<<"${kustomization}" >/dev/null && break
+    attempt=$((attempt + 1))
+    [ "${attempt}" -lt "${settle_attempts}" ] ||
+      fail "the ${layer} Kustomization has not applied its current generation with a non-empty inventory"
+    sleep "${settle_seconds}"
+  done
   if jq -e '.status.conditions // [] | any(.type == "Ready" and .status == "False")' <<<"${kustomization}" >/dev/null; then
     printf 'Note: the %s Kustomization applied its revision but an unrelated health check is failing\n' "${layer}"
   fi
diff --git a/scripts/tests/test-retire-unused-apps.sh b/scripts/tests/test-retire-unused-apps.sh
index f85748de41..396f0ec481 100755
--- a/scripts/tests/test-retire-unused-apps.sh
+++ b/scripts/tests/test-retire-unused-apps.sh
@@ -58,7 +58,8 @@ for name in "${names[@]}"; do
   file="${STATE}/${kind}/${namespace}/${name}"
   case "${verb}" in
     get)
-      if [ "${kind}" = kustomization ]; then cat "${STATE}/${name}.json" 2>/dev/null || cat "${STATE}/apps.json"; elif [ -f "${file}" ]; then cat "${file}"; fi ;;
+      if [ "${kind}" = kustomization ] && [ -f "${STATE}/${name}.first.json" ]; then cat "${STATE}/${name}.first.json"; rm -f "${STATE}/${name}.first.json";
+      elif [ "${kind}" = kustomization ]; then cat "${STATE}/${name}.json" 2>/dev/null || cat "${STATE}/apps.json"; elif [ -f "${file}" ]; then cat "${file}"; fi ;;
     delete)
       [ -n "${KEEP:-}" ] && [ "${kind}/${name}" = "${KEEP}" ] && continue
       rm -f "${file}"
@@ -127,7 +128,7 @@ run() { # <state> [env...] -> sets status and output
   local state="$1"
   shift
   if output="$(env STATE="${state}" KUBECTL="${work_dir}/kubectl" RETIREMENT_POLL_SECONDS=0 \
-    RETIREMENT_POLL_ATTEMPTS=3 RETIREMENT_CONFIRM=retire-crossview-headlamp-backstage "$@" \
+    RETIREMENT_POLL_ATTEMPTS=3 RETIREMENT_SETTLE_SECONDS=0 RETIREMENT_SETTLE_ATTEMPTS=3 RETIREMENT_CONFIRM=retire-crossview-headlamp-backstage "$@" \
     bash "${script}" 2>&1)"; then
     status=0
   else
@@ -196,6 +197,14 @@ jq '.status.conditions = [{type: "Ready", status: "False", reason: "HealthCheckF
 run "${state}"
 expect 0 'an unrelated health check is failing' 'an unrelated health failure must not block the retirement'
 
+# A layer read mid-retry (Progressing) is sampled again until it settles.
+state="$(seed retrying "${deployed}")"
+jq '.status.conditions = [{type: "Ready", status: "False", reason: "HealthCheckFailed"}]' "${state}/apps.json" >"${state}/apps.tmp" && mv "${state}/apps.tmp" "${state}/apps.json"
+jq '.status.conditions = [{type: "Ready", status: "Unknown", reason: "Progressing"}]' "${state}/apps.json" >"${state}/apps.first.json"
+run "${state}"
+expect 0 'an unrelated health check is failing' 'a layer that settles after a retry must not block the retirement'
+[ "$(grep -c '^get kustomization apps' "${state}/calls")" -ge 2 ] || fail 'a Progressing layer must be sampled again'
+
 # An object of the same name that Flux apps does not own is never deleted.
 state="$(seed foreign "${deployed}")"
 put "${state}" "${cnpg}" backstage backstage-db '{"metadata":{"labels":{}}}'