diff --git a/packages/core/src/tools/edit.test.ts b/packages/core/src/tools/edit.test.ts
index 4077a6cd41..84086bbd69 100644
--- a/packages/core/src/tools/edit.test.ts
+++ b/packages/core/src/tools/edit.test.ts
@@ -511,6 +511,42 @@ function doIt() {
       expect(result.newContent).toBe(expectedContent);
     });
 
+    it('should preserve trailing newlines in flexible replacement (regression)', async () => {
+      const content = '  line1\n  line2\n  line3\n';
+      const result = await calculateReplacement(mockConfig, {
+        params: {
+          file_path: 'test.txt',
+          old_string: 'line1\nline2',
+          new_string: 'line1-replaced\nline2-replaced',
+        },
+        currentContent: content,
+        abortSignal,
+      });
+
+      expect(result.newContent).toBe(
+        '  line1-replaced\n  line2-replaced\n  line3\n',
+      );
+    });
+
+    it('should correctly increment loop index in flexible replacement when allow_multiple is true (regression)', async () => {
+      const content = '  match1\n  match2\n  match1\n  match2\n';
+      const result = await calculateReplacement(mockConfig, {
+        params: {
+          file_path: 'test.txt',
+          old_string: 'match1\nmatch2',
+          new_string: 'replaced1\nreplaced2\nreplaced3',
+          allow_multiple: true,
+        },
+        currentContent: content,
+        abortSignal,
+      });
+
+      expect(result.occurrences).toBe(2);
+      expect(result.newContent).toBe(
+        '  replaced1\n  replaced2\n  replaced3\n  replaced1\n  replaced2\n  replaced3\n',
+      );
+    });
+
     it('should correctly rebase indentation in flexible replacement without double-indenting', async () => {
       const content = '    if (a) {\n        foo();\n    }\n';
       // old_string and new_string are unindented. They should be rebased to 4-space.
diff --git a/packages/core/src/tools/edit.ts b/packages/core/src/tools/edit.ts
index 3f6d5d9f62..c00ea4c0da 100644
--- a/packages/core/src/tools/edit.ts
+++ b/packages/core/src/tools/edit.ts
@@ -202,15 +202,19 @@ async function calculateFlexibleReplacement(
       const indentationMatch = firstLineInMatch.match(/^([ \t]*)/);
       const indentation = indentationMatch ? indentationMatch[1] : '';
       const newBlockWithIndent = applyIndentation(replaceLines, indentation);
-      sourceLines.splice(
-        i,
-        searchLinesStripped.length,
-        newBlockWithIndent.join('\n'),
-      );
-      i += replaceLines.length;
-    } else {
-      i++;
+
+      let replacementText = newBlockWithIndent.join('\n');
+      if (
+        new_string !== '' &&
+        window[window.length - 1].endsWith('\n') &&
+        !replacementText.endsWith('\n')
+      ) {
+        replacementText += '\n';
+      }
+
+      sourceLines.splice(i, searchLinesStripped.length, replacementText);
     }
+    i++;
   }
 
   if (flexibleOccurrences > 0) {