diff --git a/changelog.d/unreleased/2943.fixed.md b/changelog.d/unreleased/2943.fixed.md
new file mode 100644
index 0000000000..1c3750357c
--- /dev/null
+++ b/changelog.d/unreleased/2943.fixed.md
@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 2943
+affected:
+  - src/CodeIndex/Indexer/BoundedRegex.cs
+  - src/CodeIndex/Cli/RuntimeSafety.cs
+---
+
+## English
+
+- **SQL reference JSON tests no longer drop references under grouped net9 runs (#2943)** - bounded SQL extraction regexes now share the runtime safety timeout budget, preventing grouped net9 validation from treating transient regex timeouts as missing SQL target/source references.
+
+## 日本語
+
+- **grouped net9 実行で SQL reference JSON テストが参照を落とさなくなりました (#2943)** - SQL 抽出用の bounded regex が runtime safety の timeout 予算を共有するようになり、grouped net9 検証で一時的な regex timeout が SQL target/source 参照欠落として扱われる問題を防ぎます。
diff --git a/changelog.d/unreleased/2945.fixed.md b/changelog.d/unreleased/2945.fixed.md
new file mode 100644
index 0000000000..de18986203
--- /dev/null
+++ b/changelog.d/unreleased/2945.fixed.md
@@ -0,0 +1,17 @@
+---
+category: fixed
+issues:
+  - 2945
+affected:
+  - src/CodeIndex/Indexer/BoundedRegex.cs
+  - src/CodeIndex/Cli/RuntimeSafety.cs
+  - tests/CodeIndex.Tests/BoundedRegexTests.cs
+---
+
+## English
+
+- **Reference extraction keeps the runtime safety regex budget under full-suite load (#2945)** - bounded extractor regexes now use the same 2-second match timeout that the CLI reports for regex safety, avoiding false-negative reference extraction when local full test runs are CPU-contended.
+
+## 日本語
+
+- **full suite の高負荷時も参照抽出が runtime safety の regex 予算を使うようになりました (#2945)** - bounded extractor regex は CLI が regex safety として報告する 2 秒の match timeout と同じ値を使うようになり、CPU 競合下のローカル full test で参照抽出が false negative になる問題を避けます。
diff --git a/src/CodeIndex/Cli/RuntimeSafety.cs b/src/CodeIndex/Cli/RuntimeSafety.cs
index d21649ec12..38b5336044 100644
--- a/src/CodeIndex/Cli/RuntimeSafety.cs
+++ b/src/CodeIndex/Cli/RuntimeSafety.cs
@@ -1,10 +1,11 @@
 using System.Text.RegularExpressions;
+using CodeIndex.Indexer;
 
 namespace CodeIndex.Cli;
 
 internal static class RuntimeSafety
 {
-    internal static readonly TimeSpan RegexMatchTimeout = TimeSpan.FromSeconds(2);
+    internal static readonly TimeSpan RegexMatchTimeout = BoundedRegex.DefaultMatchTimeout;
 
     public static void Configure()
     {
diff --git a/src/CodeIndex/Indexer/BoundedRegex.cs b/src/CodeIndex/Indexer/BoundedRegex.cs
index 325cc7a37f..b606403956 100644
--- a/src/CodeIndex/Indexer/BoundedRegex.cs
+++ b/src/CodeIndex/Indexer/BoundedRegex.cs
@@ -7,7 +7,7 @@ namespace CodeIndex.Indexer;
 internal sealed class BoundedRegex : BclRegex
 {
     // Keep regex matches bounded, but leave enough scheduler headroom for full-suite CI contention.
-    internal static readonly TimeSpan DefaultMatchTimeout = TimeSpan.FromSeconds(1);
+    internal static readonly TimeSpan DefaultMatchTimeout = TimeSpan.FromSeconds(2);
 
     public BoundedRegex(string pattern)
         : base(pattern, RegexOptions.None, DefaultMatchTimeout)
diff --git a/tests/CodeIndex.Tests/BoundedRegexTests.cs b/tests/CodeIndex.Tests/BoundedRegexTests.cs
index 6b1ed8026d..9afd412900 100644
--- a/tests/CodeIndex.Tests/BoundedRegexTests.cs
+++ b/tests/CodeIndex.Tests/BoundedRegexTests.cs
@@ -1,3 +1,4 @@
+using CodeIndex.Cli;
 using CodeIndex.Indexer;
 
 namespace CodeIndex.Tests;
@@ -12,4 +13,10 @@ public void DefaultMatchTimeout_KeepsBoundedMatchesFromTimingOutUnderNormalSched
             TimeSpan.FromSeconds(1),
             TimeSpan.FromSeconds(5));
     }
+
+    [Fact]
+    public void DefaultMatchTimeout_MatchesRuntimeSafetyTimeout()
+    {
+        Assert.Equal(RuntimeSafety.RegexMatchTimeout, BoundedRegex.DefaultMatchTimeout);
+    }
 }