diff --git a/api/python/quilt3/packages.py b/api/python/quilt3/packages.py
index 0643d46840d..61139d121d1 100644
--- a/api/python/quilt3/packages.py
+++ b/api/python/quilt3/packages.py
@@ -1540,6 +1540,9 @@ def check_hash_conficts(latest_hash):
                 new_entry.hash = dict(type=SHA256_CHUNKED_HASH_NAME, value=checksum)
             pkg._set(logical_key, new_entry)
 
+        for lk, meta in self._walk_dir_meta():
+            pkg._ensure_subpackage(self._split_key(lk[:-1])).set_meta(meta)
+
         # Some entries may miss hash values (e.g because of selector_fn), so we need
         # to fix them before calculating the top hash.
         pkg._calculate_missing_hashes()