diff --git a/src/bin/pg_rewind/filemap.c b/src/bin/pg_rewind/filemap.c
index bb4ffd0e38..a2cd317c72 100644
--- a/src/bin/pg_rewind/filemap.c
+++ b/src/bin/pg_rewind/filemap.c
@@ -334,12 +334,11 @@ process_target_file(const char *path, file_type_t type, size_t oldsize,
 	file_entry_t *entry;
 
 	/*
-	 * Ignore any path matching the exclusion filters.  This is not actually
-	 * mandatory for target files, but this does not hurt and let's be
-	 * consistent with the source processing.
+	 * Do not apply any exclusion filters here, the folders marked for
+	 * deletion on the target should be entirely empty, and we also
+	 * check after pg_internal.init which is present in each database
+	 * folder.
 	 */
-	if (check_file_excluded(path, false))
-		return;
 
 	snprintf(localpath, sizeof(localpath), "%s/%s", datadir_target, path);
 	if (lstat(localpath, &statbuf) < 0)