diff --git a/.chronus/changes/witemple-msft-fix-encodedname-dup-detect-2025-9-7-15-21-36.md b/.chronus/changes/witemple-msft-fix-encodedname-dup-detect-2025-9-7-15-21-36.md
new file mode 100644
index 00000000000..88a93e23eb9
--- /dev/null
+++ b/.chronus/changes/witemple-msft-fix-encodedname-dup-detect-2025-9-7-15-21-36.md
@@ -0,0 +1,7 @@
+---
+changeKind: fix
+packages:
+  - "@typespec/compiler"
+---
+
+Addressed a bug that could cause duplicate `@encodedName` applications to be detected when none actually exist.
\ No newline at end of file
diff --git a/packages/compiler/src/lib/encoded-names.ts b/packages/compiler/src/lib/encoded-names.ts
index 3ccb45ecdd2..a7c04b792f9 100644
--- a/packages/compiler/src/lib/encoded-names.ts
+++ b/packages/compiler/src/lib/encoded-names.ts
@@ -106,7 +106,16 @@ export function validateEncodedNamesConflicts(program: Program) {
 
   for (const [target, map] of getEncodedNamesStateMap(program).entries()) {
     const scope = getScope(target);
-    if (scope === undefined) {
+    const memberValues = new Set(scope?.members.values());
+    if (
+      scope === undefined ||
+      // Workaround: exclude members that aren't actually in the scope. This can happen when types of
+      // properties, enum members, or union variants are cloned for one reason or another, but are not
+      // actually attached to the parent type. This should probably be fixed in cloning logic (mutator
+      // implementation) instead, but for now this workaround solves some problems with false positives
+      // in duplication tracking here.
+      !memberValues.has(target)
+    ) {
       return;
     }
     for (const [mimeType, name] of map.entries()) {
diff --git a/packages/compiler/src/lib/visibility.ts b/packages/compiler/src/lib/visibility.ts
index b746dd3b4e2..591919c77d9 100644
--- a/packages/compiler/src/lib/visibility.ts
+++ b/packages/compiler/src/lib/visibility.ts
@@ -681,7 +681,7 @@ function createVisibilityFilterMutator(
             realm.remove(clone);
             modified = true;
           } else {
-            const mutated = mutateSubgraph(program, [mpMutator], prop);
+            const mutated = cachedMutateSubgraph(program, mpMutator, prop);
 
             clone.properties.set(key, mutated.type as ModelProperty);