diff --git a/src/scripts/set_pou_code.py b/src/scripts/set_pou_code.py
index ddeda46..d804d42 100644
--- a/src/scripts/set_pou_code.py
+++ b/src/scripts/set_pou_code.py
@@ -3,6 +3,11 @@ import sys, scriptengine as script_engine, os, traceback
 POU_FULL_PATH = "{POU_FULL_PATH}" # Expecting format like "Application/MyPOU" or "Folder/SubFolder/MyPOU"
 DECLARATION_CONTENT = """{DECLARATION_CONTENT}"""
 IMPLEMENTATION_CONTENT = """{IMPLEMENTATION_CONTENT}"""
+# Boolean flags from the TS wrapper. "True" if the caller passed the field,
+# "False" if they omitted it. Empty string is a valid intentional value
+# (e.g. "wipe declaration") and must not be conflated with "not provided".
+SET_DECLARATION = {SET_DECLARATION}
+SET_IMPLEMENTATION = {SET_IMPLEMENTATION}
 
 try:
     print("DEBUG: set_pou_code script: POU_FULL_PATH='%s', Project='%s'" % (POU_FULL_PATH, PROJECT_FILE_PATH))
@@ -18,9 +23,7 @@ try:
 
     # --- Set Declaration Part ---
     declaration_updated = False
-    # Check if the content is actually provided (might be None/empty if only impl is set)
-    has_declaration_content = 'DECLARATION_CONTENT' in locals() or 'DECLARATION_CONTENT' in globals()
-    if has_declaration_content and DECLARATION_CONTENT is not None: # Check not None
+    if SET_DECLARATION:
         if hasattr(target_object, 'textual_declaration'):
             decl_obj = target_object.textual_declaration
             if decl_obj and hasattr(decl_obj, 'replace'):
@@ -37,13 +40,12 @@ try:
         else:
             print("WARN: Target '%s' does not have textual_declaration attribute. Skipping declaration update." % target_name)
     else:
-         print("DEBUG: Declaration content not provided or is None. Skipping declaration update.")
+         print("DEBUG: Declaration not provided by caller (SET_DECLARATION=False). Skipping declaration update.")
 
 
     # --- Set Implementation Part ---
     implementation_updated = False
-    has_implementation_content = 'IMPLEMENTATION_CONTENT' in locals() or 'IMPLEMENTATION_CONTENT' in globals()
-    if has_implementation_content and IMPLEMENTATION_CONTENT is not None: # Check not None
+    if SET_IMPLEMENTATION:
         if hasattr(target_object, 'textual_implementation'):
             impl_obj = target_object.textual_implementation
             if impl_obj and hasattr(impl_obj, 'replace'):
@@ -60,7 +62,7 @@ try:
         else:
             print("WARN: Target '%s' does not have textual_implementation attribute. Skipping implementation update." % target_name)
     else:
-        print("DEBUG: Implementation content not provided or is None. Skipping implementation update.")
+        print("DEBUG: Implementation not provided by caller (SET_IMPLEMENTATION=False). Skipping implementation update.")
 
 
     # --- SAVE THE PROJECT TO PERSIST THE CODE CHANGE ---
diff --git a/src/server.ts b/src/server.ts
index f28eb5a..f10bab8 100644
--- a/src/server.ts
+++ b/src/server.ts
@@ -843,6 +843,11 @@ export async function startMcpServer(config: ServerConfig): Promise<void> {
       // Escape for triple-quoted Python strings
       const sanDecl = (args.declarationCode ?? '').replace(/\\/g, '\\\\').replace(/"""/g, '\\"\\"\\"');
       const sanImpl = (args.implementationCode ?? '').replace(/\\/g, '\\\\').replace(/"""/g, '\\"\\"\\"');
+      // Distinguish "argument provided" from "argument is empty string". An
+      // omitted declaration must NOT reach decl_obj.replace('') -- doing so
+      // wipes the POU's PROGRAM/VAR...END_VAR block, leaving an UNKNOWN POU.
+      const setDecl = args.declarationCode !== undefined ? 'True' : 'False';
+      const setImpl = args.implementationCode !== undefined ? 'True' : 'False';
       const script = scriptManager.prepareScriptWithHelpers(
         'set_pou_code',
         {
@@ -850,6 +855,8 @@ export async function startMcpServer(config: ServerConfig): Promise<void> {
           POU_FULL_PATH: sanPouPath,
           DECLARATION_CONTENT: sanDecl,
           IMPLEMENTATION_CONTENT: sanImpl,
+          SET_DECLARATION: setDecl,
+          SET_IMPLEMENTATION: setImpl,
         },
         ['ensure_project_open', 'find_object_by_path']
       );
diff --git a/tests/integration/e2e.test.ts b/tests/integration/e2e.test.ts
index f22c960..6ec224d 100644
--- a/tests/integration/e2e.test.ts
+++ b/tests/integration/e2e.test.ts
@@ -58,11 +58,40 @@ describe('E2E Script Preparation', () => {
         POU_FULL_PATH: 'Application/MyPOU',
         DECLARATION_CONTENT: sanDecl,
         IMPLEMENTATION_CONTENT: sanImpl,
+        SET_DECLARATION: 'True',
+        SET_IMPLEMENTATION: 'True',
       },
       ['ensure_project_open', 'find_object_by_path']
     );
     expect(script).toContain('Application/MyPOU');
     expect(script).toContain('x := 42;');
+    expect(script).toContain('SET_DECLARATION = True');
+    expect(script).toContain('SET_IMPLEMENTATION = True');
+  });
+
+  it('set_pou_code with omitted declarationCode gates the replace() call', () => {
+    // Regression: when caller omits declarationCode, the script must NOT
+    // call decl_obj.replace('') -- doing so wipes the POU's
+    // PROGRAM/VAR...END_VAR block (binary becomes UNKNOWN POU).
+    // server.ts passes SET_DECLARATION='False' in that case.
+    const script = mgr.prepareScriptWithHelpers(
+      'set_pou_code',
+      {
+        PROJECT_FILE_PATH: 'C:\\test.project',
+        POU_FULL_PATH: 'Application/PLC_PRG',
+        DECLARATION_CONTENT: '',
+        IMPLEMENTATION_CONTENT: 'x := 1;',
+        SET_DECLARATION: 'False',
+        SET_IMPLEMENTATION: 'True',
+      },
+      ['ensure_project_open', 'find_object_by_path']
+    );
+    expect(script).toContain('SET_DECLARATION = False');
+    expect(script).toContain('SET_IMPLEMENTATION = True');
+    // The skip branch must be reachable
+    expect(script).toContain('SET_DECLARATION=False');
+    // No leftover {PLACEHOLDER} unsubstituted
+    expect(script).not.toMatch(/\{[A-Z_]+\}/);
   });
 
   it('check_status script has no placeholders after load', () => {