diff --git a/system/src/Grav/Common/Page/Pages.php b/system/src/Grav/Common/Page/Pages.php
index 58d387962..766331782 100644
--- a/system/src/Grav/Common/Page/Pages.php
+++ b/system/src/Grav/Common/Page/Pages.php
@@ -699,6 +699,9 @@ class Pages
         if (\is_string($instance)) {
             $instance = $this->flex ? $this->flex->getObject($instance) : null;
         }
+        if ($instance && !$instance instanceof PageInterface) {
+            throw new \RuntimeException('Routing failed on unknown type', 500);
+        }
 
         return $instance;
     }
@@ -1271,7 +1274,7 @@ class Pages
         $config = $this->grav['config'];
 
         // TODO: right now we are just emulating normal pages, it is inefficient and bad... but works!
-        $collection = $directory->getCollection();
+        $collection = $directory->getIndex();
         $cache = $directory->getCache('index');
 
         /** @var Language $language */
@@ -1293,8 +1296,9 @@ class Pages
 
         $this->grav['debugger']->addMessage('Page cache missed, rebuilding pages..');
 
-        $root = $collection->getRoot();
-        $instances = [$root->path() => $root];
+        $root = $this->buildRootPage();
+        $root_path = $root->path();
+        $instances = [$root_path => $root];
 
         if ($config->get('system.pages.events.page')) {
             $this->grav->fireEvent('onBuildPagesInitialized');
@@ -1312,6 +1316,9 @@ class Pages
             }
 
             $path = $page->path();
+            if ($path === $root_path) {
+                continue;
+            }
             $parent = dirname($path);
 
             $instances[$path] = $page->getFlexKey();
@@ -1322,7 +1329,10 @@ class Pages
         }
 
         foreach ($children as $path => $list) {
-            $page = $instances[$path];
+            $page = $instances[$path] ?? null;
+            if (null === $page) {
+                continue;
+            }
             if ($config->get('system.pages.events.page')) {
                 $this->grav->fireEvent('onFolderProcessed', new Event(['page' => $page]));
             }
diff --git a/system/src/Grav/Framework/Flex/FlexIndex.php b/system/src/Grav/Framework/Flex/FlexIndex.php
index 49f99e04e..2f992bc51 100644
--- a/system/src/Grav/Framework/Flex/FlexIndex.php
+++ b/system/src/Grav/Framework/Flex/FlexIndex.php
@@ -579,7 +579,7 @@ class FlexIndex extends ObjectIndex implements FlexCollectionInterface, FlexInde
      * @param array $entries    Updated index
      * @return array            Compiled list of entries
      */
-    protected static function updateIndexFile(FlexStorageInterface $storage, array $index, array $entries): array
+    protected static function updateIndexFile(FlexStorageInterface $storage, array $index, array $entries, array $options = []): array
     {
         // Calculate removed objects.
         $removed = array_diff_key($index, $entries);
@@ -621,12 +621,12 @@ class FlexIndex extends ObjectIndex implements FlexCollectionInterface, FlexInde
         // Go through all the updated objects and refresh their index data.
         $updated = $added = [];
         foreach ($rows as $key => $row) {
-            if (null !== $row) {
+            if (null !== $row || !empty($options['include_missing'])) {
                 $entry = $entries[$key] + ['key' => $key];
                 if ($keyField !== 'storage_key' && isset($row[$keyField])) {
                     $entry['key'] = $row[$keyField];
                 }
-                static::updateIndexData($entry, $row);
+                static::updateIndexData($entry, $row ?? []);
                 if (isset($row['__error'])) {
                     $entry['__error'] = true;
                     static::onException(new \RuntimeException(sprintf('Object failed to load: %s (%s)', $key, $row['__error'])));