diff --git a/lib/core/public/configure.js b/lib/core/public/configure.js
index 0915c981e..499bb6d6a 100644
--- a/lib/core/public/configure.js
+++ b/lib/core/public/configure.js
@@ -9,6 +9,16 @@ function configure(spec) {
     throw new Error('No audit configured');
   }
 
+  // [a11y-critical]: configure() reports success by not throwing and returns
+  // nothing, so a caller cannot tell a completed registration from one that was
+  // later discarded (see load.js — a second axe evaluation replaces _audit).
+  // Record what this call registered so that is answerable after the fact.
+  const configureLog = {
+    ruleCountBefore: audit.rules.length,
+    rulesIn: Array.isArray(spec.rules) ? spec.rules.length : 0,
+    checksIn: Array.isArray(spec.checks) ? spec.checks.length : 0
+  };
+
   if (spec.axeVersion || spec.ver) {
     const specVersion = spec.axeVersion || spec.ver;
     if (!/^\d+\.\d+\.\d+(-canary)?/.test(specVersion)) {
@@ -139,6 +149,12 @@ function configure(spec) {
   if (spec.crossOriginDenylist) {
     audit.setCrossOriginDenylist(spec.crossOriginDenylist);
   }
+
+  // [a11y-critical]: completes the record started above. audit.generation lets a
+  // caller detect that the audit it configured is no longer the live one.
+  configureLog.ruleCountAfter = audit.rules.length;
+  configureLog.generation = audit.generation;
+  audit.lastConfigure = configureLog;
 }
 
 export default configure;
diff --git a/lib/core/public/load.js b/lib/core/public/load.js
index ea69f3b69..c599e04bf 100644
--- a/lib/core/public/load.js
+++ b/lib/core/public/load.js
@@ -12,7 +12,19 @@ import mergeErrors from '../utils/merge-errors';
  * @private
  */
 export default function load(audit) {
+  // [a11y-critical]: this discards every prior axe.configure() with no error —
+  // the built axe.js calls _load on evaluation, so evaluating axe twice in one
+  // context silently resets the registry to stock. Carry a generation counter so
+  // a caller can tell its configured audit was replaced out from under it.
+  const previous = axe._audit;
   axe._audit = new Audit(audit);
+  axe._audit.generation = previous ? (previous.generation || 0) + 1 : 0;
+  if (previous && typeof axe.log === 'function') {
+    axe.log(
+      'axe._load replaced an existing audit; previously configured rules and checks are gone',
+      { generation: axe._audit.generation }
+    );
+  }
 }
 
 function runCommand(data, keepalive, callback) {
diff --git a/lib/core/utils/normalize-run-options.js b/lib/core/utils/normalize-run-options.js
index 1c65d518c..d163902bd 100644
--- a/lib/core/utils/normalize-run-options.js
+++ b/lib/core/utils/normalize-run-options.js
@@ -1,6 +1,6 @@
 /**
  * Ensure all rules that are expected to run exist
- * @throws {Error} If any tag or rule specified in options is unknown
+ * @throws {Error} If any rule specified in options.runOnly is unknown
  * @param  {Object} options  Options object
  * @return {Object}          Validated options object
  */
@@ -69,11 +69,13 @@ export default function normalizeRunOptions(options = {}) {
     }
   }
   if (typeof options.rules === 'object') {
-    Object.keys(options.rules).forEach(ruleId => {
-      if (!ruleIds.includes(ruleId)) {
-        throw new Error('unknown rule `' + ruleId + '` in options.rules');
-      }
-    });
+    // [a11y-critical]: log unknown ids in options.rules instead of throwing
+    const unmatchedRules = Object.keys(options.rules).filter(
+      ruleId => !ruleIds.includes(ruleId)
+    );
+    if (unmatchedRules.length !== 0) {
+      axe.log('Could not find rules `' + unmatchedRules.join('`, `') + '`');
+    }
   }
   return options;
 }
diff --git a/test/core/utils/normalize-run-options.js b/test/core/utils/normalize-run-options.js
index 67b472d83..daffced4c 100644
--- a/test/core/utils/normalize-run-options.js
+++ b/test/core/utils/normalize-run-options.js
@@ -213,8 +213,21 @@ describe('axe.utils.normalizeRunOptions', () => {
     });
   });
 
-  it('throws an error when option.rules has an unknown rule', () => {
-    assert.throws(() => {
+  it('logs an issue when option.rules has an unknown rule', () => {
+    let message = '';
+    axe._setLogger(m => {
+      message = m;
+    });
+    axe.utils.normalizeRunOptions({
+      rules: {
+        fakeRule: { enabled: false }
+      }
+    });
+    assert.include(message, 'Could not find rules');
+  });
+
+  it('does not throw when option.rules has an unknown rule', () => {
+    assert.doesNotThrow(() => {
       axe.utils.normalizeRunOptions({
         rules: {
           fakeRule: { enabled: false }
@@ -223,6 +236,16 @@ describe('axe.utils.normalizeRunOptions', () => {
     });
   });
 
+  it('keeps known rules in options.rules when another id is unknown', () => {
+    const options = axe.utils.normalizeRunOptions({
+      rules: {
+        'color-contrast': { enabled: false },
+        fakeRule: { enabled: false }
+      }
+    });
+    assert.deepEqual(options.rules['color-contrast'], { enabled: false });
+  });
+
   it('logs an issue when a tag is unknown', () => {
     let message = '';
     axe._setLogger(m => {