diff --git a/src/internal/kopia/upload.go b/src/internal/kopia/upload.go
index bae4896c4..faa46cea8 100644
--- a/src/internal/kopia/upload.go
+++ b/src/internal/kopia/upload.go
@@ -908,6 +908,11 @@ func inflateBaseTree(
 
 		ent, err := snapshotfs.GetNestedEntry(ctx, dir, pathElems)
 		if err != nil {
+			if isErrEntryNotFound(err) {
+				logger.Ctx(ctx).Infow("base snapshot missing subtree", "error", err)
+				continue
+			}
+
 			return errors.Wrapf(err, "snapshot %s getting subtree root", snap.ID)
 		}
 
diff --git a/src/internal/kopia/upload_test.go b/src/internal/kopia/upload_test.go
index 20cd66cb6..0b33e8db6 100644
--- a/src/internal/kopia/upload_test.go
+++ b/src/internal/kopia/upload_test.go
@@ -2261,6 +2261,110 @@ func (suite *HierarchyBuilderUnitSuite) TestBuildDirectoryTreeSkipsDeletedSubtre
 	expectTree(t, ctx, expected, dirTree)
 }
 
+func (suite *HierarchyBuilderUnitSuite) TestBuildDirectoryTree_HandleEmptyBase() {
+	tester.LogTimeOfTest(suite.T())
+	t := suite.T()
+
+	ctx, flush := tester.NewContext()
+	defer flush()
+
+	var (
+		archiveStorePath = makePath(
+			suite.T(),
+			[]string{testTenant, service, testUser, category, testArchiveID},
+			false)
+		archiveLocPath = makePath(
+			suite.T(),
+			[]string{testTenant, service, testUser, category, testArchiveDir},
+			false)
+	)
+
+	// baseSnapshot with the following layout:
+	// - a-tenant
+	//   - exchangeMetadata
+	//     - user1
+	//       - email
+	//         - file1
+	getBaseSnapshot := func() fs.Entry {
+		return baseWithChildren(
+			[]string{
+				testTenant,
+				path.ExchangeMetadataService.String(),
+				testUser,
+				category,
+			},
+			[]fs.Entry{
+				virtualfs.StreamingFileWithModTimeFromReader(
+					encodeElements(testFileName)[0],
+					time.Time{},
+					io.NopCloser(bytes.NewReader(testFileData)),
+				),
+			},
+		)
+	}
+
+	// Metadata subtree doesn't appear because we don't select it as one of the
+	// subpaths and we're not passing in a metadata collection.
+	expected := expectedTreeWithChildren(
+		[]string{
+			testTenant,
+			service,
+			testUser,
+			category,
+		},
+		[]*expectedNode{
+			{
+				name: testArchiveID,
+				children: []*expectedNode{
+					{
+						name:     testFileName2,
+						children: []*expectedNode{},
+					},
+				},
+			},
+		},
+	)
+
+	progress := &corsoProgress{
+		pending: map[string]*itemDetails{},
+		errs:    fault.New(true),
+	}
+	mc := mockconnector.NewMockExchangeCollection(archiveStorePath, archiveLocPath, 1)
+	mc.ColState = data.NewState
+	mc.Names[0] = testFileName2
+	mc.Data[0] = testFileData2
+
+	msw := &mockSnapshotWalker{
+		snapshotRoot: getBaseSnapshot(),
+	}
+
+	collections := []data.BackupCollection{mc}
+
+	// Returned directory structure should look like:
+	// - a-tenant
+	//   - exchangeMetadata
+	//     - user1
+	//       - emails
+	//         - file1
+	//   - exchange
+	//     - user1
+	//       - emails
+	//         - Archive
+	//           - file2
+	dirTree, err := inflateDirTree(
+		ctx,
+		msw,
+		[]IncrementalBase{
+			mockIncrementalBase("", testTenant, testUser, path.ExchangeService, path.EmailCategory),
+		},
+		collections,
+		nil,
+		progress)
+	require.NoError(t, err)
+
+	expectTree(t, ctx, expected, dirTree)
+}
+
 type mockMultiSnapshotWalker struct {
 	snaps map[string]fs.Entry
 }
diff --git a/src/internal/kopia/wrapper.go b/src/internal/kopia/wrapper.go
index 0c4f690fa..f40823a4c 100644
--- a/src/internal/kopia/wrapper.go
+++ b/src/internal/kopia/wrapper.go
@@ -331,7 +331,7 @@ func getItemStream(
 		encodeElements(itemPath.PopFront().Elements()...),
 	)
 	if err != nil {
-		if strings.Contains(err.Error(), "entry not found") {
+		if isErrEntryNotFound(err) {
 			err = clues.Stack(data.ErrNotFound, err).WithClues(ctx)
 		}
 
@@ -492,3 +492,8 @@ func (w Wrapper) FetchPrevSnapshotManifests(
 
 	return fetchPrevSnapshotManifests(ctx, w.c, reasons, tags), nil
 }
+
+func isErrEntryNotFound(err error) bool {
+	return strings.Contains(err.Error(), "entry not found") &&
+		!strings.Contains(err.Error(), "parent is not a directory")
+}
diff --git a/src/internal/tester/config.go b/src/internal/tester/config.go
index d79d95104..7681646d9 100644
--- a/src/internal/tester/config.go
+++ b/src/internal/tester/config.go
@@ -111,7 +111,7 @@ func readTestConfig() (map[string]string, error) {
 		TestCfgUserID,
 		os.Getenv(EnvCorsoM365TestUserID),
 		vpr.GetString(TestCfgUserID),
-		"conneri@8qzvrj.onmicrosoft.com",
+		"pradeepg@8qzvrj.onmicrosoft.com",
 	)
 	fallbackTo(
 		testEnv,
@@ -132,7 +132,7 @@ func readTestConfig() (map[string]string, error) {
 		TestCfgLoadTestOrgUsers,
 		os.Getenv(EnvCorsoM365LoadTestOrgUsers),
 		vpr.GetString(TestCfgLoadTestOrgUsers),
-		"lidiah@8qzvrj.onmicrosoft.com,conneri@8qzvrj.onmicrosoft.com",
+		"lidiah@8qzvrj.onmicrosoft.com,pradeepg@8qzvrj.onmicrosoft.com",
 	)
 	fallbackTo(
 		testEnv,