diff --git a/scripts/lib/test-projects.mjs b/scripts/lib/test-projects.mjs
index 13026a798f..3275860297 100644
--- a/scripts/lib/test-projects.mjs
+++ b/scripts/lib/test-projects.mjs
@@ -11,12 +11,15 @@ export const SOURCE_TEST_PROJECTS = [
     name: "services",
     group: "source",
     include: ["src/application/**/*.test.ts"],
+    exclude: ["src/application/EvidenceBundleFiles.test.ts"],
   },
   {
     name: "adapters",
     group: "source",
     include: [
       "src/*.test.ts",
+      // This application fixture replaces a module and needs a fresh graph.
+      "src/application/EvidenceBundleFiles.test.ts",
       "src/{android,apkSignature,apktool,jeb,adb,artifacts,browser,config,cutter,dotnet,electron,erlang,evm,firmware,flutter,pcap,ghidra,go,gpu,hopper,ida,inspector,javascript,main,native,process,python,reference,rust,server,sqlite,wasm,windows}/**/*.test.ts",
     ],
   },
@@ -66,6 +69,7 @@ export const BUILT_TEST_PROJECTS = [
     name: "mcp-boundary",
     group: "built",
     include: ["tests/boundary/mcp/**/*.test.ts"],
+    exclude: ["tests/boundary/mcp/javascriptAnalysisCancellation.test.ts"],
   },
   {
     name: "acceptance",
@@ -75,7 +79,10 @@ export const BUILT_TEST_PROJECTS = [
   {
     name: "process-global",
     group: "built",
-    include: ["tests/process-global/**/*.test.ts"],
+    include: [
+      "tests/process-global/**/*.test.ts",
+      "tests/boundary/mcp/javascriptAnalysisCancellation.test.ts",
+    ],
   },
 ];
 
diff --git a/tests/boundary/filesystem/ciTestProjects.test.ts b/tests/boundary/filesystem/ciTestProjects.test.ts
index 1f20ef2d94..fab5017bd5 100644
--- a/tests/boundary/filesystem/ciTestProjects.test.ts
+++ b/tests/boundary/filesystem/ciTestProjects.test.ts
@@ -143,6 +143,20 @@ describe("canonical test-project ownership", () => {
 });
 
 describe("test module isolation", () => {
+  it.each([
+    ["src/application/EvidenceBundleFiles.test.ts", "adapters", "source"],
+    [
+      "tests/boundary/mcp/javascriptAnalysisCancellation.test.ts",
+      "process-global",
+      "built",
+    ],
+  ])(
+    "keeps %s isolated without changing its preparation group",
+    (path, name, group) => {
+      expect(projectForTest(path)).toMatchObject({ name, group });
+    },
+  );
+
   it("keeps module mocks out of projects that share one module graph", async () => {
     // A mock registered after another file in the same worker loaded the
     // module never applies, so the test's outcome depends on file scheduling.