diff --git a/src/application/ClientConfigurationDocument.capacity.test.ts b/src/application/ClientConfigurationDocument.capacity.test.ts
index e8670bdd09..190435a363 100644
--- a/src/application/ClientConfigurationDocument.capacity.test.ts
+++ b/src/application/ClientConfigurationDocument.capacity.test.ts
@@ -9,6 +9,50 @@ import {
 const registration = { command: "rea", args: ["mcp"] };
 
 describe("TOML configuration source capacity", () => {
+  it.each(["\n", "\r\n"])(
+    "retains adjacent assignments and multiline values with %j breaks",
+    (newline) => {
+      const prefix = Array.from(
+        { length: 128 },
+        (_, index) =>
+          `[foreign.entry_${index}]\nvalue = ${index}\nnote = """first\n# [mcp_servers.rea]\nlast"""\nitems = [\n${index},\n]\n`,
+      ).join("");
+      // Include a BOM, an empty value, and a final statement without a newline.
+      const original =
+        "\uFEFF" +
+        `${prefix}[mcp_servers.rea]\ncommand = "previous"\n[tail]\nempty = ""\nlast = 7`.replaceAll(
+          "\n",
+          newline,
+        );
+      const parsed = parseClientConfiguration(original, "toml");
+      const desired = withClientServers(parsed, {
+        ...parsed.servers,
+        rea: registration,
+      });
+      const configured = serializeClientConfiguration(
+        desired,
+        "toml",
+        original,
+      );
+      expect(
+        configured.startsWith("\uFEFF" + prefix.replaceAll("\n", newline)),
+      ).toBe(true);
+      expect(parseClientConfiguration(configured, "toml").document).toEqual(
+        desired,
+      );
+      const removed = serializeClientConfiguration(
+        withClientServers(parsed, {}),
+        "toml",
+        configured,
+      );
+      const expectedForeignDocument = { ...parsed.document };
+      delete expectedForeignDocument.mcp_servers;
+      expect(parseClientConfiguration(removed, "toml").document).toEqual(
+        expectedForeignDocument,
+      );
+    },
+  );
+
   it("retains a large multiline foreign value inside an inline server table", () => {
     const note = `first\n${"x\n".repeat(500_000)}last`;
     const original = `mcp_servers = { other = {command="other",env={NOTE="""${note}"""}}}\n`;
diff --git a/src/application/ClientConfigurationDocument.ts b/src/application/ClientConfigurationDocument.ts
index 2fb2ee35f0..48724bf1c7 100644
--- a/src/application/ClientConfigurationDocument.ts
+++ b/src/application/ClientConfigurationDocument.ts
@@ -975,12 +975,6 @@ const upsertTomlServerSection = (
     appendLines(pending);
     pending.length = 0;
   };
-  const lineIndexAt = (offset: number): number => {
-    let line = 0;
-    for (let index = 0; index < lineStarts.length; index += 1)
-      if ((lineStarts[index] ?? 0) <= offset) line = index;
-    return line;
-  };
   let lineIndex = 0;
   while (lineIndex < lines.length) {
     const physical = lines[lineIndex] ?? "";
@@ -1015,7 +1009,14 @@ const upsertTomlServerSection = (
       let statementEnd = valueEnd;
       while (statementEnd < text.length && text[statementEnd] !== "\n")
         statementEnd += 1;
-      const endLine = lineIndexAt(Math.max(statementEnd - 1, lineStart));
+      const lastOffset = Math.max(statementEnd - 1, lineStart);
+      let endLine = lineIndex;
+      // Statements advance through the source; only inspect their own lines.
+      while (
+        endLine + 1 < lineStarts.length &&
+        (lineStarts[endLine + 1] ?? 0) <= lastOffset
+      )
+        endLine += 1;
       if (skipping) {
         discardPending();
         lineIndex = endLine + 1;