Is there an existing issue for this?

• I have searched the existing issues

This issue exists in the latest npm version

• I am using the latest npm

This is not just a request to bump a dependency for a CVE

• This is not solely a request to bump a dependency for a CVE

Current Behavior

When a patch fails and the install is run with --ignore-patch-failures, the package is installed unpatched and the lockfile records no patched entry for it — but package.json still declares the patchedDependencies entry. The two artifacts now disagree: a subsequent npm ci fails with the generic out-of-sync EUSAGE error (while a plain npm install re-attempts and fails with EPATCHFAILED).

Expected Behavior

Failing on a genuinely broken patch is reasonable. But the resulting state — a lockfile that is immediately npm ci-invalid against its own unchanged package.json — is surprising. A clearer message tying the out-of-sync state back to the skipped patch would help.

Steps To Reproduce

REPRO=/tmp/patch-ignore-fail && rm -rf "$REPRO" && mkdir -p "$REPRO" && cd "$REPRO"
cat > package.json <<'EOF'
{ "name": "ipf", "version": "1.0.0", "dependencies": { "is-positive": "3.1.0" } }
EOF
npm install --no-audit --no-fund

mkdir -p patches
cat > patches/[email protected] <<'EOF'
--- a/index.js
+++ b/index.js
@@ -1,3 +1,4 @@
 NONEXISTENT
+x
 fake
 lines
EOF
node -e "const fs=require('fs');const p=require('./package.json'); \
  p.patchedDependencies={'[email protected]':'patches/[email protected]'}; \
  fs.writeFileSync('package.json',JSON.stringify(p,null,2))"

npm install --no-audit --no-fund --ignore-patch-failures   # warns, installs unpatched
npm ci --no-audit --no-fund                                # => EUSAGE: not in sync

Observed

The --ignore-patch-failures install succeeds with a warning and writes a lockfile with no patched entry; npm ci then fails with EUSAGE (out of sync) against the unchanged package.json.

Expected

Either the artifacts stay consistent, or the npm ci failure message ties the out-of-sync state back to the skipped patch.

Environment

• npm: 12.0.0-pre.0
• Node.js: v24.15.0
• OS Name: Darwin 25.5.0 (macOS, arm64)
• Relevant config: none — reproduces with default configuration