diff --git a/src/org/labkey/test/TestFileUtils.java b/src/org/labkey/test/TestFileUtils.java
index d73ad973a1..892ae635b8 100644
--- a/src/org/labkey/test/TestFileUtils.java
+++ b/src/org/labkey/test/TestFileUtils.java
@@ -38,6 +38,7 @@
 import org.bouncycastle.openpgp.operator.jcajce.JcePBEDataDecryptorFactoryBuilder;
 import org.bouncycastle.util.io.Streams;
 import org.jetbrains.annotations.NotNull;
+import org.junit.Assert;
 import org.labkey.api.util.FileUtil;
 import org.jetbrains.annotations.Nullable;
 import org.openqa.selenium.NotFoundException;
@@ -445,6 +446,31 @@ public static void deleteDir(File dir)
         }
     }
 
+    /**
+     * Rename a directory.
+     * @param sourceDir the directory to rename
+     * @param newDirName the new name for the directory
+     * @return return the path to the renamed directory
+     */
+    public static Path renameDir(Path sourceDir, String newDirName) throws IOException
+    {
+        LOG.info("Renaming {} to {}", sourceDir, newDirName);
+
+        // Check if the directory is outside the test enlistment.
+        checkFileLocation(sourceDir.toFile());
+
+        Assert.assertTrue("Directory does not exist: " + sourceDir, sourceDir.toFile().exists());
+
+        Path newDir = sourceDir.getParent() != null
+                ? sourceDir.getParent().resolve(newDirName)
+                : Paths.get(newDirName);
+        Files.move(sourceDir, newDir);
+
+        LOG.info("Renamed {} to {}", sourceDir, newDir);
+
+        return newDir;
+    }
+
     private static void checkFileLocation(File file)
     {
         try
@@ -452,7 +478,8 @@ private static void checkFileLocation(File file)
             if (!FileUtils.directoryContains(getLabKeyRoot(), file))
             {
                 // TODO: Consider throwing IllegalArgumentException
-                LOG.info("DEBUG: Attempting to delete a file outside of test enlistment: " + getLabKeyRoot());
+                LOG.info("DEBUG: Attempting to delete / rename a file, {}, outside of test enlistment {}.",
+                        file, getLabKeyRoot());
             }
         }
         catch (IOException ignore) { }
diff --git a/src/org/labkey/test/tests/assay/AssayTransformMissingParentDirTest.java b/src/org/labkey/test/tests/assay/AssayTransformMissingParentDirTest.java
index 69c8a94f29..137b6844a1 100644
--- a/src/org/labkey/test/tests/assay/AssayTransformMissingParentDirTest.java
+++ b/src/org/labkey/test/tests/assay/AssayTransformMissingParentDirTest.java
@@ -1,5 +1,7 @@
 package org.labkey.test.tests.assay;
 
+import org.apache.commons.io.FileUtils;
+import org.junit.Assert;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.labkey.api.util.FileUtil;
@@ -16,6 +18,7 @@
 import java.io.File;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.UUID;
 
 /**
  * Issue 54156: Regression test to ensure a reasonable error message is shown when an assay design references
@@ -29,7 +32,7 @@ public void testMissingParentDirectoryRegression() throws Exception
     {
         // Create a nested directory and an R transform script within it
         String assayName = "missingParentDirAssay";
-        Path parentDir = Files.createTempDirectory("assay-transform-parent-");
+        Path parentDir = Files.createTempDirectory("assay-transform-missing-parent-");
         Path nestedDir = FileUtil.createDirectories(parentDir.resolve("child"), false);
         String scriptName = "transformMissingParent.R";
         String transformContent = "library(Rlabkey);";
@@ -45,8 +48,17 @@ public void testMissingParentDirectoryRegression() throws Exception
         assayDesignerPage.addTransformScript(transformFile);
         assayDesignerPage.clickSave();
 
-        // Now delete the parent dir to ensure we handle it reasonably
-        TestFileUtils.deleteDir(parentDir.toFile());
+        // Rename the parent dir to ensure we handle it reasonably. Deleting directories on Windows is not always
+        // timely, renaming the directory will have the same effect.
+        String newName = "Not-Here-" + UUID.randomUUID();
+        Path renamedDir = TestFileUtils.renameDir(parentDir, newName);
+
+        Assert.assertFalse(String.format("Directory %s is still present.", parentDir),
+                FileUtils.isDirectory(parentDir.toFile()));
+
+        // Delete the renamed directory as a cleanup step. Since the directory has been renamed, the slow delete on Windows
+        // will not cause the test to fail.
+        TestFileUtils.deleteDir(renamedDir.toFile());
 
         // Attempt to import data and verify a reasonable error message is shown
         String importData = """