diff --git a/.changeset/fix-fmodata-clearoldfiles-preserve-customizations.md b/.changeset/fix-fmodata-clearoldfiles-preserve-customizations.md
new file mode 100644
index 0000000..4a07308
--- /dev/null
+++ b/.changeset/fix-fmodata-clearoldfiles-preserve-customizations.md
@@ -0,0 +1,7 @@
+---
+"@proofkit/typegen": patch
+---
+
+Fix fmodata type generation to preserve existing field-level customizations even when `clearOldFiles` is enabled.
+
+Stale files in the output directory are now removed after regeneration, so dead generated files are still cleaned up without discarding validator customizations from existing schemas.
diff --git a/packages/typegen/src/fmodata/generateODataTypes.ts b/packages/typegen/src/fmodata/generateODataTypes.ts
index 7e3edce..deaa063 100644
--- a/packages/typegen/src/fmodata/generateODataTypes.ts
+++ b/packages/typegen/src/fmodata/generateODataTypes.ts
@@ -1055,16 +1055,12 @@ export async function generateODataTypes(
   const resolvedOutputPath = resolve(cwd, outputPath);
   await mkdir(resolvedOutputPath, { recursive: true });
 
-  if (clearOldFiles) {
-    // Clear the directory if requested (but keep the directory itself)
-    fs.emptyDirSync(resolvedOutputPath);
-  }
-
   // Create ts-morph project for file manipulation
   const project = new Project({});
 
   // Generate one file per table occurrence
   const exportStatements: string[] = [];
+  const keptFiles = new Set<string>();
 
   for (const generated of generatedTOs) {
     const fileName = `${sanitizeFileName(generated.varName)}.ts`;
@@ -1072,7 +1068,7 @@ export async function generateODataTypes(
 
     // Check if file exists and parse it
     let existingFields: ParsedTableOccurrence | undefined;
-    if (fs.existsSync(filePath) && !clearOldFiles) {
+    if (fs.existsSync(filePath)) {
       try {
         const existingSourceFile = project.addSourceFileAtPath(filePath);
         const parsed = parseExistingTableFile(existingSourceFile);
@@ -1389,6 +1385,7 @@ export async function generateODataTypes(
     project.createSourceFile(filePath, fileContent, {
       overwrite: true,
     });
+    keptFiles.add(filePath);
 
     // Collect export statement for index file
     exportStatements.push(`export { ${regenerated.varName} } from "./${sanitizeFileName(regenerated.varName)}";`);
@@ -1406,7 +1403,32 @@ ${exportStatements.join("\n")}
   project.createSourceFile(indexPath, indexContent, {
     overwrite: true,
   });
+  keptFiles.add(indexPath);
 
   // Format and save files
   await formatAndSaveSourceFiles(project, cwd);
+
+  if (clearOldFiles) {
+    // For fmodata generation, preserve customizations by merging first,
+    // then remove files/directories that were not regenerated this run.
+    const keepSet = new Set(Array.from(keptFiles).map((p) => resolve(p)));
+    const deleteStaleEntries = (dirPath: string): void => {
+      const entries = fs.readdirSync(dirPath, { withFileTypes: true });
+      for (const entry of entries) {
+        const entryPath = resolve(dirPath, entry.name);
+        if (entry.isDirectory()) {
+          deleteStaleEntries(entryPath);
+          const remainingEntries = fs.readdirSync(entryPath);
+          if (remainingEntries.length === 0 && !keepSet.has(entryPath)) {
+            fs.removeSync(entryPath);
+          }
+          continue;
+        }
+        if (!keepSet.has(entryPath)) {
+          fs.removeSync(entryPath);
+        }
+      }
+    };
+    deleteStaleEntries(resolvedOutputPath);
+  }
 }
diff --git a/packages/typegen/tests/e2e/fmodata-preserve-customizations.test.ts b/packages/typegen/tests/e2e/fmodata-preserve-customizations.test.ts
index 19c8d74..2c3fb3f 100644
--- a/packages/typegen/tests/e2e/fmodata-preserve-customizations.test.ts
+++ b/packages/typegen/tests/e2e/fmodata-preserve-customizations.test.ts
@@ -270,4 +270,54 @@ describe("fmodata generateODataTypes preserves user customizations", () => {
       await fs.rm(tmpDir, { recursive: true, force: true });
     }
   });
+
+  it("preserves custom validators and removes stale files when clearOldFiles is true", async () => {
+    const tmpDir = await fs.mkdtemp(path.join(os.tmpdir(), "proofkit-fmodata-preserve-"));
+
+    try {
+      const entitySetName = "MyTable";
+      const entityTypeName = "NS.MyTable";
+      const metadata = makeMetadata({
+        entitySetName,
+        entityTypeName,
+        fields: [{ name: "FieldA", type: "Edm.String", fieldId: "F1" }],
+      });
+
+      const existingFilePath = path.join(tmpDir, "MyTable.ts");
+      await fs.writeFile(
+        existingFilePath,
+        [
+          `import { fmTableOccurrence, textField } from "@proofkit/fmodata";`,
+          `import { z } from "zod/v4";`,
+          "",
+          `export const MyTable = fmTableOccurrence("MyTable", {`,
+          `  "FieldA": textField().inputValidator(z.string()).entityId("F1"),`,
+          "});",
+          "",
+        ].join("\n"),
+        "utf8",
+      );
+
+      const staleFilePath = path.join(tmpDir, "OldTable.ts");
+      await fs.writeFile(staleFilePath, `export const OldTable = "stale";\n`, "utf8");
+
+      await generateODataTypes(metadata, {
+        type: "fmodata",
+        path: tmpDir,
+        clearOldFiles: true,
+        tables: [{ tableName: "MyTable" }],
+      });
+
+      const regenerated = await fs.readFile(existingFilePath, "utf8");
+      expect(regenerated).toContain(`FieldA: textField().entityId("F1").inputValidator(z.string())`);
+
+      const staleExists = await fs
+        .access(staleFilePath)
+        .then(() => true)
+        .catch(() => false);
+      expect(staleExists).toBe(false);
+    } finally {
+      await fs.rm(tmpDir, { recursive: true, force: true });
+    }
+  });
 });