diff --git a/GVFS/GVFS.Common/ModifiedPathsDatabase.cs b/GVFS/GVFS.Common/ModifiedPathsDatabase.cs
index 5a7e34c43..95fb18e73 100644
--- a/GVFS/GVFS.Common/ModifiedPathsDatabase.cs
+++ b/GVFS/GVFS.Common/ModifiedPathsDatabase.cs
@@ -52,6 +52,31 @@ public static bool TryLoadOrCreate(ITracer tracer, string dataDirectory, Physica
             return true;
         }
 
+        /// <summary>
+        /// This method will examine the modified paths to check if there is already a parent folder entry in
+        /// the modified paths.  If there is a parent folder the entry does not need to be in the modified paths
+        /// and will be removed because the parent folder is recursive and covers any children.
+        /// </summary>
+        public void RemoveEntriesWithParentFolderEntry(ITracer tracer)
+        {
+            int startingCount = this.modifiedPaths.Count;
+            using (ITracer activity = tracer.StartActivity(nameof(this.RemoveEntriesWithParentFolderEntry), EventLevel.Informational))
+            {
+                foreach (string modifiedPath in this.modifiedPaths)
+                {
+                    if (this.ContainsParentDirectory(modifiedPath))
+                    {
+                        this.modifiedPaths.TryRemove(modifiedPath);
+                    }
+                }
+
+                EventMetadata metadata = new EventMetadata();
+                metadata.Add(nameof(startingCount), startingCount);
+                metadata.Add("EndCount", this.modifiedPaths.Count);
+                activity.Stop(metadata);
+            }
+        }
+
         public bool Contains(string path, bool isFolder)
         {
             string entry = this.NormalizeEntryString(path, isFolder);
diff --git a/GVFS/GVFS.FunctionalTests/Tests/EnlistmentPerTestCase/ModifiedPathsTests.cs b/GVFS/GVFS.FunctionalTests/Tests/EnlistmentPerTestCase/ModifiedPathsTests.cs
index f8e42331e..f2f255180 100644
--- a/GVFS/GVFS.FunctionalTests/Tests/EnlistmentPerTestCase/ModifiedPathsTests.cs
+++ b/GVFS/GVFS.FunctionalTests/Tests/EnlistmentPerTestCase/ModifiedPathsTests.cs
@@ -37,11 +37,6 @@ public class ModifiedPathsTests : TestsWithEnlistmentPerTestCase
                 $"A {RenameNewDotGitFileTarget}",
                 $"A {FileToCreateOutsideRepo}",
                 $"A {FolderToCreateOutsideRepo}/",
-                $"A {FolderToDelete}/CreateCommonAssemblyVersion.bat",
-                $"A {FolderToDelete}/CreateCommonCliAssemblyVersion.bat",
-                $"A {FolderToDelete}/CreateCommonVersionHeader.bat",
-                $"A {FolderToDelete}/RunFunctionalTests.bat",
-                $"A {FolderToDelete}/RunUnitTests.bat",
                 $"A {FolderToDelete}/",
             };
 
@@ -138,9 +133,16 @@ public void ModifiedPathsSavedAfterRemount(FileSystemRunner fileSystem)
             folderToCreateOutsideRepoTargetPath.ShouldBeADirectory(fileSystem);
             folderToCreateOutsideRepoPath.ShouldNotExistOnDisk(fileSystem);
 
-            string folderToDelete = this.Enlistment.GetVirtualPathTo(FolderToDelete);
-            fileSystem.DeleteDirectory(folderToDelete);
-            folderToDelete.ShouldNotExistOnDisk(fileSystem);
+            string folderToDeleteFullPath = this.Enlistment.GetVirtualPathTo(FolderToDelete);
+            fileSystem.WriteAllText(Path.Combine(folderToDeleteFullPath, "NewFile.txt"), "Contents for new file");
+            string newFileToDelete = Path.Combine(folderToDeleteFullPath, "NewFileToDelete.txt");
+            fileSystem.WriteAllText(newFileToDelete, "Contents for new file");
+            fileSystem.DeleteFile(newFileToDelete);
+            fileSystem.WriteAllText(Path.Combine(folderToDeleteFullPath, "CreateCommonVersionHeader.bat"), "Changing the file contents");
+            fileSystem.DeleteFile(Path.Combine(folderToDeleteFullPath, "RunUnitTests.bat"));
+
+            fileSystem.DeleteDirectory(folderToDeleteFullPath);
+            folderToDeleteFullPath.ShouldNotExistOnDisk(fileSystem);
 
             // Remount
             this.Enlistment.UnmountGVFS();
diff --git a/GVFS/GVFS.UnitTests/Common/ModifiedPathsDatabaseTests.cs b/GVFS/GVFS.UnitTests/Common/ModifiedPathsDatabaseTests.cs
index 663a76bb0..40bacf08f 100644
--- a/GVFS/GVFS.UnitTests/Common/ModifiedPathsDatabaseTests.cs
+++ b/GVFS/GVFS.UnitTests/Common/ModifiedPathsDatabaseTests.cs
@@ -1,6 +1,7 @@
 using GVFS.Common;
 using GVFS.Tests.Should;
 using GVFS.UnitTests.Mock;
+using GVFS.UnitTests.Mock.Common;
 using GVFS.UnitTests.Mock.FileSystem;
 using NUnit.Framework;
 using System;
@@ -17,6 +18,21 @@ public class ModifiedPathsDatabaseTests
         private const string ExistingEntries = @"A file.txt
 A dir/file2.txt
 A dir1/dir2/file3.txt
+";
+        private const string EntriesToCompress = @"A file.txt
+D deleted.txt
+A dir/file2.txt
+A dir/dir3/dir4/
+A dir1/dir2/file3.txt
+A dir/
+D deleted/
+A dir1/dir2/
+A dir1/file.txt
+A dir1/dir2/dir3/dir4/dir5/
+A dir/dir2/file3.txt
+A dir/dir4/dir5/
+D dir/dir2/deleted.txt
+A dir1/dir2
 ";
 
         [TestCase]
@@ -119,6 +135,19 @@ public void EntryNotAddedIfParentDirectoryExists()
             modifiedPathsDatabase.Contains("dir2/dir", isFolder: true).ShouldBeTrue();
         }
 
+        [TestCase]
+        public void RemoveEntriesWithParentFolderEntry()
+        {
+            ModifiedPathsDatabase modifiedPathsDatabase = CreateModifiedPathsDatabase(EntriesToCompress);
+            modifiedPathsDatabase.RemoveEntriesWithParentFolderEntry(new MockTracer());
+            modifiedPathsDatabase.Count.ShouldEqual(5);
+            modifiedPathsDatabase.Contains("file.txt", isFolder: false).ShouldBeTrue();
+            modifiedPathsDatabase.Contains("dir/", isFolder: true).ShouldBeTrue();
+            modifiedPathsDatabase.Contains("dir1/dir2", isFolder: false).ShouldBeTrue();
+            modifiedPathsDatabase.Contains("dir1/dir2/", isFolder: true).ShouldBeTrue();
+            modifiedPathsDatabase.Contains("dir1/file.txt", isFolder: false).ShouldBeTrue();
+        }
+
         private static void TestAddingPath(string path, bool isFolder = false)
         {
             TestAddingPath(path, path, isFolder);
diff --git a/GVFS/GVFS.Virtualization/FileSystemCallbacks.cs b/GVFS/GVFS.Virtualization/FileSystemCallbacks.cs
index d7c0d57b4..627c895a5 100644
--- a/GVFS/GVFS.Virtualization/FileSystemCallbacks.cs
+++ b/GVFS/GVFS.Virtualization/FileSystemCallbacks.cs
@@ -171,6 +171,9 @@ public static bool IsPathInsideDotGit(string relativePath)
 
         public bool TryStart(out string error)
         {
+            this.modifiedPaths.RemoveEntriesWithParentFolderEntry(this.context.Tracer);
+            this.modifiedPaths.WriteAllEntriesAndFlush();
+
             if (!this.fileSystemVirtualizer.TryStart(this, out error))
             {
                 return false;