diff --git a/reme/components/file_chunker/json_file_chunker.py b/reme/components/file_chunker/json_file_chunker.py
index e8cce166..f1249260 100644
--- a/reme/components/file_chunker/json_file_chunker.py
+++ b/reme/components/file_chunker/json_file_chunker.py
@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import json
+from io import StringIO
 from pathlib import Path
 from typing import Any
 
@@ -137,10 +138,10 @@ class JsonFileChunker(BaseFileChunker):
                     [chunk],
                 )
             else:
-                lines = raw_text.split("\n", keepends=True)
+                lines = StringIO(raw_text)
                 chunked_lines = [{"text": "", "start_line": 1, "end_line": 1}]
                 for idx, line in enumerate(lines):
-                    if len(chunked_lines[-1]["text"]) + len(line) > self.chunk_chars:
+                    if chunked_lines[-1]["text"] and len(chunked_lines[-1]["text"]) + len(line) > self.chunk_chars:
                         chunked_lines.append({"text": "", "start_line": idx + 1, "end_line": idx + 1})
                     chunked_lines[-1]["text"] += line
                     chunked_lines[-1]["end_line"] = idx + 1
diff --git a/tests/unit/test_background_steps.py b/tests/unit/test_background_steps.py
index 87867a5b..3e5ae579 100644
--- a/tests/unit/test_background_steps.py
+++ b/tests/unit/test_background_steps.py
@@ -25,7 +25,7 @@ from watchfiles import Change
 
 from reme.components import R
 from reme.components.agent_wrapper import BaseAgentWrapper
-from reme.components.file_chunker import DefaultFileChunker
+from reme.components.file_chunker import DefaultFileChunker, JsonFileChunker
 from reme.components.file_catalog import LocalFileCatalog
 from reme.components.file_store import LocalFileStore
 from reme.components.runtime_context import RuntimeContext
@@ -885,6 +885,58 @@ def test_update_index_modified_file_reuses_unchanged_embedding():
     asyncio.run(run())
 
 
+def test_update_index_replaces_large_malformed_json_without_changing_source():
+    """Malformed JSON uses the fallback and replaces its old chunks."""
+
+    async def run():
+        with tempfile.TemporaryDirectory() as tmpdir, temp_chdir(tmpdir):
+            cwd = Path.cwd()
+            source = cwd / "daily" / "broken.json"
+            sibling = cwd / "daily" / "healthy.json"
+            original = ("{" + "x" * 2000).encode()
+            replacement = ("{" + "y" * 2000).encode()
+            source.parent.mkdir(parents=True)
+            source.write_bytes(original)
+            sibling.write_text('{"healthy": true}', encoding="utf-8")
+            fs = LocalFileStore(name="default", embedding_store="")
+            chunker = JsonFileChunker(supported_extensions=["json"], chunk_chars=256)
+            await fs.start()
+            await chunker.start()
+            try:
+                app_ctx = _make_app_context(cwd)
+                app_ctx.components = {ComponentEnum.FILE_CHUNKER: {"json": chunker}}
+                step = UpdateIndexStep(file_store=fs, persist=False, app_context=app_ctx)
+                response = await step(
+                    RuntimeContext(
+                        changes=[
+                            {"change": "added", "path": str(source)},
+                            {"change": "added", "path": str(sibling)},
+                        ],
+                    ),
+                )
+
+                assert response.success is True
+                assert source.read_bytes() == original
+                nodes = {node.path: node for node in await fs.get_nodes()}
+                old_chunk_ids = nodes["daily/broken.json"].chunk_ids
+                assert nodes["daily/healthy.json"].chunk_ids
+
+                source.write_bytes(replacement)
+                response = await step(RuntimeContext(changes=[{"change": "modified", "path": str(source)}]))
+
+                assert response.success is True
+                assert source.read_bytes() == replacement
+                nodes = {node.path: node for node in await fs.get_nodes()}
+                assert nodes["daily/broken.json"].chunk_ids != old_chunk_ids
+                assert all(chunk_id not in fs.file_chunks for chunk_id in old_chunk_ids)
+                assert nodes["daily/healthy.json"].chunk_ids
+            finally:
+                await chunker.close()
+                await fs.close()
+
+    asyncio.run(run())
+
+
 def test_update_index_skips_oversized_file_and_clears_stale_index():
     """Oversized content is not read and any previous index entry is removed."""
 
diff --git a/tests/unit/test_json_file_chunker.py b/tests/unit/test_json_file_chunker.py
index 4d8af06a..597da053 100644
--- a/tests/unit/test_json_file_chunker.py
+++ b/tests/unit/test_json_file_chunker.py
@@ -255,6 +255,35 @@ class TestEdgeCases:
         assert len(chunks) == 1
         assert chunks[0].start_line == 1
 
+    @pytest.mark.parametrize("length", [2000, 2001])
+    def test_large_malformed_fallback_preserves_a_single_long_line(self, make_json, length):
+        text = "{" + "x" * (length - 1)
+        path = make_json(raw=text)
+
+        node, chunks = _run(JsonFileChunker().chunk(path))
+
+        assert "".join(chunk.text for chunk in chunks) == text
+        assert all(chunk.text for chunk in chunks)
+        assert node.chunk_ids == [chunk.id for chunk in chunks]
+        assert [(chunk.start_line, chunk.end_line) for chunk in chunks] == [(1, 1)]
+
+    @pytest.mark.parametrize("ending", ["", "\n", "\r\n"])
+    def test_large_malformed_fallback_preserves_lf_lines_and_endings(self, make_json, ending):
+        text = "first\r\n" + "é\u2028middle\u2029" + "x" * 300 + ending
+        path = make_json(raw="")
+        with open(path, "wb") as file:
+            file.write(text.encode())
+
+        node, chunks = _run(JsonFileChunker(chunk_chars=256).chunk(path))
+
+        with open(path, "rb") as file:
+            assert file.read() == text.encode()
+        with open(path, encoding="utf-8") as file:
+            assert "".join(chunk.text for chunk in chunks) == file.read()
+        assert all(chunk.text for chunk in chunks)
+        assert node.chunk_ids == [chunk.id for chunk in chunks]
+        assert [(chunk.start_line, chunk.end_line) for chunk in chunks] == [(1, 1), (2, 2)]
+
     def test_chunk_chars_floor(self):
         assert JsonFileChunker(chunk_chars=10).chunk_chars == 256