diff -u b/includes/bootstrap.inc b/includes/bootstrap.inc
--- b/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -835,9 +835,9 @@
 function drupal_get_filename($type, $name, $filename = NULL) {
   // The location of files will not change during the request, so do not use
   // drupal_static().
-  // The $files static variable will hold the locations of all requested files,
-  // and any file that gets added during the request will have been checked
-  // with a file_exists() at some point.
+  // The $files static variable will hold the locations of all requested files.
+  // We can be sure that any file listed in this static variable actually
+  // exists as all additions have gone through a file_exists() check.
   static $files = array();
 
   // Profiles are a special case: they have a fixed location and naming.
@@ -854,14 +854,15 @@
     $files[$type][$name] = $filename;
   }
   elseif (isset($files[$type][$name])) {
-    // This item had already been found earlier in the request, either in this
-    // same function or by the static cache having been primed elsewhere, such
-    // as in system_list(). Do nothing.
+    // This item had already been found earlier in the request, either through
+    // priming of the static cache (i.e. in system_list()), through a lookup
+    // in the {system} table, or through a file scan (cached or not).
+    // Do nothing.
   }
   else {
     $system_filepaths = &drupal_static('system_filepaths');
     if (!isset($system_filepaths[$type][$name])) {
-      // Look for the file name listed in the {system} table.
+      // Look for the filename listed in the {system} table.
       // Verify that we have an active database connection, before querying
       // the database. This is required because this function is called both
       // before we have a database connection (i.e. during installation) and
@@ -886,8 +887,8 @@
         // hide the error completely.
       }
     }
-    // Fallback to searching the filesystem if the database could not find the
-    // file or the filename returned by the database is not found.
+    // Fall back to searching the filesystem if the database could not find the
+    // file or the file does not exist at the path returned by the database.
     if (!isset($files[$type][$name])) {
       $files[$type][$name] = _drupal_get_filename_fallback($type, $name);
     }
@@ -895,9 +896,9 @@
 
   if (isset($files[$type][$name])) {
     // We found a file.
-    // Clean up the item from the file scan cache, in case the item had been
-    // marked as missing or moved.
     $file_scans = &drupal_static('_drupal_get_filename_fallback');
+    // If this file had previously been marked as missing or moved, clean up
+    // the entry from the file scan cache.
     if (isset($file_scans[$type][$name])) {
       $file_scans[$type][$name] = NULL;
       $file_scans['#write_cache'] = TRUE;
@@ -909,9 +910,10 @@
 /**
  * Helper function for drupal_get_filename().
  *
- * This triggers a file scan, caching any missing or moved files. If an item
- * had been marked as missing or moved in a previous file scan, no new file
- * scans will be performed.
+ * This function looks for the requested file by triggering a file scan,
+ * caching the new location if the file has moved and caching the miss
+ * if the file is missing. If a file had been marked as missing or moved
+ * in a previous file scan, no new file scan will be performed.
  *
  * @param string $type
  *   The type of the item (theme, theme_engine, module, profile).
@@ -924,25 +926,27 @@
 function _drupal_get_filename_fallback($type, $name) {
   // This static variable will hold all missing and moved files, in order
   // to prevent unnecessary file scans. It is an associative array with as
-  // keys the file type and name, and as value the boolean FALSE if the
-  // module is missing, or a string with location found in a file scan if
-  // the module has moved from the location listed in the {system} table.
+  // keys the type and name of the item, and as value:
+  // - the boolean FALSE if the item is missing
+  // - a string with location found in a file scan if the module/theme has moved
+  // from the location listed in the {system} table.
   $file_scans = &drupal_static('_drupal_get_filename_fallback');
   if (!isset($file_scans)) {
     $file_scans = array();
   }
-  // Get the missing and moved files from persistent cache, if available.
+  // Get the list of files marked as missing and moved during earlier file scans
+  // from the persistent cache, if available.
   if (!isset($file_scans['#cache_merge_done'])) {
     try {
       if (function_exists('cache_get')) {
         $cache = cache_get('_drupal_get_filename_fallback', 'cache_bootstrap');
         if (!empty($cache->data)) {
-          // Merge the changes already done in the current request
-          // (including the setting of missing records to NULL) into the
-          // values saved in persistent cache.
+          // Merge the changes to the file scan cache done in the current
+          // request (including the setting of previously set records to NULL)
+          // with the values that had been stored in the persistent cache.
           $file_scans = drupal_array_merge_deep($cache->data, $file_scans);
-          // Set a flag so we know that we've already done a merge with
-          // the values in persistent cache.
+          // Set a flag so we remember that we've done a merge with the values
+          // stored in the persistent cache.
           $file_scans['#cache_merge_done'] = TRUE;
         }
       }
@@ -952,7 +956,7 @@
     }
   }
 
-  // Check whether this file had previously moved from its location in the
+  // Check whether this file had previously moved from the path listed in the
   // {system} table.
   if (isset($file_scans[$type][$name]) && is_string($file_scans[$type][$name]) && file_exists($file_scans[$type][$name])) {
     // We found the file at the cached location.
@@ -964,15 +968,15 @@
     $filename_from_file_scan = _drupal_get_filename_perform_file_scan($type, $name);
   }
   if (isset($filename_from_file_scan)) {
-    // Check whether the current file was listed as being in another
+    // Check whether the file we found was listed as being in another
     // location in the {system} table.
     $system_filepaths = &drupal_static('system_filepaths');
     if (isset($system_filepaths[$type][$name]) && $system_filepaths[$type][$name] != $filename_from_file_scan) {
-      // This file has moved. Cache its new location into the missing and
-      // moved files list.
+      // This file has moved. Store its new location in the file scan 
+      // cache.
       $file_scans[$type][$name] = $filename_from_file_scan[$type][$name];
-      // Make sure our change to the missing and moved files list will be
-      // written to persistent cache.
+      // Make sure our change to the file scan cache will be written to
+      // the persistent cache.
       $file_scans['#write_cache'] = TRUE;
       trigger_error(format_string('The following %type has moved on the file system: %name. In order to fix this, clear caches or put the file back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('%type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
     }
@@ -980,9 +984,9 @@
   }
   else {
     trigger_error(format_string('The following %type is missing from the file system: %name. In order to fix this, put the file back in its original location or uninstall the module. For more information, see <a href="@documentation">the documentation page</a>.', array('%type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
-    // Make sure our change to the missing files list will be written to
-    // persistent cache.
-    if (!isset($file_scans[$type][$name])) {
+    // Make sure our change to the file scan cache will be written to
+    // the persistent cache.
+    if (!(isset($file_scans[$type][$name]) && $file_scans[$type][$name] === FALSE)) {
       $file_scans['#write_cache'] = TRUE;
     }
     // Mark the file as missing.
@@ -1022,7 +1026,7 @@
   // Check if we had already scanned this directory/extension combination.
   if (!isset($dirs[$dir][$extension])) {
     // Log that we have now scanned this directory/extension combination
-    // into a static variable to prevent unnecessary scans.
+    // into a static variable so as to prevent unnecessary file scans.
     $dirs[$dir][$extension] = TRUE;
     if (!function_exists('drupal_system_listing')) {
       require_once DRUPAL_ROOT . '/includes/common.inc';
@@ -1046,17 +1050,21 @@
 }
 
 /**
- * Writes the missing and moved files to persistent cache.
+ * Writes the file scan cache to the persistent cache.
+ *
+ * This cache stores all files marked as missing or moved after a file scan
+ * to prevent unnecessary file scans in subsequent requests. This cache is
+ * cleared in system_list_reset() (i.e. after a module/theme rebuild).
  */
 function drupal_file_scan_write_cache() {
-  // Only write to cache if we are fully bootstrapped.
+  // Only write to the persistent cache if we are fully bootstrapped.
   if (drupal_get_bootstrap_phase() != DRUPAL_BOOTSTRAP_FULL) {
     return;
   }
   $file_scans = &drupal_static('_drupal_get_filename_fallback');
   if (isset($file_scans['#write_cache'])) {
     // Merge the newly found out missing and moved file data with
-    // the previously existing data, if we hadn't done so yet.
+    // the previously existing data, if we had not done so yet.
     if (!isset($file_scans['#cache_merge_done'])) {
       $cache = cache_get('_drupal_get_filename_fallback', 'cache_bootstrap');
       if (isset($cache->data)) {
@@ -1064,6 +1072,7 @@
       }
     }
     $file_scans['#write_cache'] = NULL;
+    $file_scans['#cache_merge_done'] = NULL;
     cache_set('_drupal_get_filename_fallback', $file_scans, 'cache_bootstrap');
   }
 }