diff --git a/src/application/ReferenceSourceImportEntries.test.ts b/src/application/ReferenceSourceImportEntries.test.ts
index 70dab2e31c..3bd85788f6 100644
--- a/src/application/ReferenceSourceImportEntries.test.ts
+++ b/src/application/ReferenceSourceImportEntries.test.ts
@@ -640,3 +640,27 @@ it("prefers a later exact filename over an earlier unique canonical candidate",
     expect.objectContaining({ to: `${composed}.js`, resolution: "internal" }),
   ]);
 });
+
+it("retains a missing target's directory requirement when rebasing from the inventory root", () => {
+  const read: ReferenceSourceRead = {
+    root: "/selected",
+    entries: [
+      {
+        status: "read",
+        kind: "symlink",
+        path: "nested/link",
+        target: "sub/missing/",
+        targetState: "missing",
+      },
+    ],
+    bytesRead: 0,
+    limitations: [],
+  };
+  expect(parseReferenceSourceEntries(read, []).entries).toContainEqual(
+    expect.objectContaining({
+      path: "nested/link",
+      target: "../sub/missing/",
+      target_state: "missing",
+    }),
+  );
+});
diff --git a/src/application/ReferenceSourceImportEntries.ts b/src/application/ReferenceSourceImportEntries.ts
index 69462c09d2..ac05eb7e16 100644
--- a/src/application/ReferenceSourceImportEntries.ts
+++ b/src/application/ReferenceSourceImportEntries.ts
@@ -6,6 +6,7 @@ import type { JavaScriptPackageType } from "../domain/javascript/javascriptSourc
 import { logicalPathEscapesRoot } from "../domain/artifactIdentity.js";
 import {
   createReferenceSourcePathLookup,
+  rebaseReferenceSourceTarget,
   decodeReferenceSourceModuleUrlPath,
   isPortableAbsoluteReferenceTarget,
   type ReferenceSourcePathLookup,
@@ -630,7 +631,7 @@ const appendReadEntry = (
       entry.targetState === "internal" ||
       (entry.targetState === "missing" &&
         !isPortableAbsoluteReferenceTarget(entry.target))
-        ? posix.relative(posix.dirname(entry.path), entry.target) || "."
+        ? rebaseReferenceSourceTarget(entry.path, entry.target)
         : entry.target,
     target_state: entry.targetState,
     classifications,
diff --git a/src/domain/referenceSourcePathIdentity.ts b/src/domain/referenceSourcePathIdentity.ts
index 9a1718973d..d6473cff87 100644
--- a/src/domain/referenceSourcePathIdentity.ts
+++ b/src/domain/referenceSourcePathIdentity.ts
@@ -75,3 +75,12 @@ export const decodeReferenceSourceModuleUrlPath = (
     );
   }
 };
+
+/** Rebase a portable target without discarding its directory-required suffix. */
+export const rebaseReferenceSourceTarget = (
+  linkPath: string,
+  target: string,
+): string => {
+  const relative = posix.relative(posix.dirname(linkPath), target) || ".";
+  return target.endsWith("/") ? `${relative}/` : relative;
+};