diff --git a/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java b/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java
index a973831e134..d28f33b6507 100644
--- a/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java
+++ b/src/main/java/org/jabref/logic/pdf/search/PdfIndexer.java
@@ -280,7 +280,7 @@ private void addToIndex(BibEntry entry, LinkedFile linkedFile, boolean shouldCom
      */
     public Set<String> getListOfFilePaths() {
         Set<String> paths = new HashSet<>();
-        try (IndexReader reader = DirectoryReader.open(indexWriter)) {
+        try (IndexReader reader = DirectoryReader.open(getIndexWriter())) {
             IndexSearcher searcher = new IndexSearcher(reader);
             MatchAllDocsQuery query = new MatchAllDocsQuery();
             TopDocs allDocs = searcher.search(query, Integer.MAX_VALUE);
diff --git a/src/main/java/org/jabref/logic/pdf/search/PdfIndexerManager.java b/src/main/java/org/jabref/logic/pdf/search/PdfIndexerManager.java
index 3f4bca38c49..8b620c015c9 100644
--- a/src/main/java/org/jabref/logic/pdf/search/PdfIndexerManager.java
+++ b/src/main/java/org/jabref/logic/pdf/search/PdfIndexerManager.java
@@ -62,16 +62,20 @@ public static void shutdownAllIndexers() {
                 LOGGER.debug("Problem closing PDF indexer", e);
             }
         });
+        indexerMap.clear();
+        pathFilePreferencesMap.clear();
     }
 
     public static void shutdownIndexer(BibDatabaseContext context) {
-        PdfIndexer indexer = indexerMap.get(context.getFulltextIndexPath());
+        Path fulltextIndexPath = context.getFulltextIndexPath();
+        PdfIndexer indexer = indexerMap.remove(fulltextIndexPath);
         if (indexer != null) {
             try {
                 indexer.close();
             } catch (IOException e) {
                 LOGGER.debug("Could not close indexer", e);
             }
+            pathFilePreferencesMap.remove(fulltextIndexPath);
         } else {
             LOGGER.debug("No indexer found for context {}", context);
         }