diff --git a/cli/src/commands/sync/sync.ts b/cli/src/commands/sync/sync.ts
index 9a0c319cf8..a6f526804d 100644
--- a/cli/src/commands/sync/sync.ts
+++ b/cli/src/commands/sync/sync.ts
@@ -104,6 +104,7 @@ import {
   getModuleFolderSuffix,
   isModuleEntryPoint,
   getScriptBasePathFromModulePath,
+  hasWrongFormatSuffix,
 } from "../../utils/resource_folders.ts";
 
 // Merge CLI options with effective settings, preserving CLI flags as overrides
@@ -1263,11 +1264,22 @@ export async function elementsToMap(
 ): Promise<{ [key: string]: string }> {
   const map: { [key: string]: string } = {};
   const processedBasePaths = new Set<string>();
+  const wrongFormatPaths: string[] = [];
   // Cache git branch at the start to avoid repeated execSync calls per file
   const cachedBranch = branchOverride ?? getCurrentGitBranch() ?? undefined;
   for await (const entry of readDirRecursiveWithIgnore(ignore, els)) {
     // console.log("FOO", entry.path, entry.ignored, entry.isDirectory)
-    if (entry.isDirectory || entry.ignored) {
+    if (entry.isDirectory) {
+      // Check for folder suffix format mismatch (only for local paths)
+      if (!isRemote) {
+        const dirName = entry.path.split(SEP).pop() ?? "";
+        if (hasWrongFormatSuffix(dirName)) {
+          wrongFormatPaths.push(entry.path);
+        }
+      }
+      continue;
+    }
+    if (entry.ignored) {
       continue;
     }
     const path = entry.path;
@@ -1442,6 +1454,20 @@ export async function elementsToMap(
     }
     // Note: branch-specific files for other branches are already filtered out earlier
   }
+
+  if (wrongFormatPaths.length > 0) {
+    const isNonDotted = getNonDottedPaths();
+    const foundFormat = isNonDotted ? ".flow/.app/.raw_app" : "__flow/__app/__raw_app";
+    const expectedFormat = isNonDotted ? "__flow/__app/__raw_app" : ".flow/.app/.raw_app";
+    const configHint = isNonDotted
+      ? "Either remove 'nonDottedPaths: true' from wmill.yaml, or rename these directories to use __flow/__app/__raw_app format."
+      : "Either add 'nonDottedPaths: true' to wmill.yaml, or rename these directories to use .flow/.app/.raw_app format.";
+    const pathList = wrongFormatPaths.map((p) => `  ${p}`).join("\n");
+    throw new Error(
+      `Found ${wrongFormatPaths.length} directory(ies) using ${foundFormat} format, but wmill.yaml expects ${expectedFormat}:\n${pathList}\n${configHint}`
+    );
+  }
+
   return map;
 }
 
diff --git a/cli/src/utils/resource_folders.ts b/cli/src/utils/resource_folders.ts
index f720fdc680..8a72a8b9ff 100644
--- a/cli/src/utils/resource_folders.ts
+++ b/cli/src/utils/resource_folders.ts
@@ -156,6 +156,24 @@ export function getMetadataPathSuffix(
 // Path Detection Functions
 // ============================================================================
 
+/**
+ * Check if a directory name uses the *wrong* folder suffix format for the
+ * current nonDottedPaths setting. Returns the resource type if mismatched,
+ * null if the name is fine (or not a resource folder at all).
+ *
+ * - nonDottedPaths=false (dotted mode): flags __flow, __app, __raw_app
+ * - nonDottedPaths=true  (non-dotted):  flags .flow, .app, .raw_app
+ */
+export function hasWrongFormatSuffix(dirName: string): FolderResourceType | null {
+  const wrongSuffixes = _nonDottedPaths ? DOTTED_SUFFIXES : NON_DOTTED_SUFFIXES;
+  for (const [type, suffix] of Object.entries(wrongSuffixes)) {
+    if (dirName.endsWith(suffix)) {
+      return type as FolderResourceType;
+    }
+  }
+  return null;
+}
+
 /** Normalize path separators to forward slash for cross-platform matching */
 function normalizeSep(p: string): string {
   return p.replaceAll("\\", "/");
diff --git a/cli/test/sync_pull_push.test.ts b/cli/test/sync_pull_push.test.ts
index 93f42bee54..07f3e9226b 100644
--- a/cli/test/sync_pull_push.test.ts
+++ b/cli/test/sync_pull_push.test.ts
@@ -41,6 +41,7 @@ import {
   isFlowInlineScriptPath,
   isRawAppBackendPath,
   getModuleFolderSuffix,
+  hasWrongFormatSuffix,
 } from "../src/utils/resource_folders.ts";
 import { newPathAssigner } from "../windmill-utils-internal/src/path-utils/path-assigner.ts";
 
@@ -1240,6 +1241,32 @@ test("setNonDottedPaths and getNonDottedPaths work correctly", () => {
   expect(getNonDottedPaths()).toEqual(false);
 });
 
+test("hasWrongFormatSuffix detects mismatched folder suffixes", () => {
+  // In dotted mode (default), non-dotted dirs are wrong
+  setNonDottedPaths(false);
+  expect(hasWrongFormatSuffix("my_flow__flow")).toEqual("flow");
+  expect(hasWrongFormatSuffix("my_app__app")).toEqual("app");
+  expect(hasWrongFormatSuffix("my_raw_app__raw_app")).toEqual("raw_app");
+  // Correct format should return null
+  expect(hasWrongFormatSuffix("my_flow.flow")).toBeNull();
+  expect(hasWrongFormatSuffix("my_app.app")).toBeNull();
+  expect(hasWrongFormatSuffix("my_raw_app.raw_app")).toBeNull();
+  // Non-resource dirs return null
+  expect(hasWrongFormatSuffix("some_folder")).toBeNull();
+  expect(hasWrongFormatSuffix("node_modules")).toBeNull();
+
+  // In non-dotted mode, dotted dirs are wrong
+  setNonDottedPaths(true);
+  expect(hasWrongFormatSuffix("my_flow.flow")).toEqual("flow");
+  expect(hasWrongFormatSuffix("my_app.app")).toEqual("app");
+  expect(hasWrongFormatSuffix("my_raw_app.raw_app")).toEqual("raw_app");
+  // Correct format should return null
+  expect(hasWrongFormatSuffix("my_flow__flow")).toBeNull();
+  expect(hasWrongFormatSuffix("my_app__app")).toBeNull();
+  expect(hasWrongFormatSuffix("my_raw_app__raw_app")).toBeNull();
+  setNonDottedPaths(false); // Reset
+});
+
 // =============================================================================
 // nonDottedPaths Fixture Functions
 // =============================================================================