diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
index 6412b1a1283c..0062a2a94aca 100644
--- a/lib/galaxy/tools/parameters/dynamic_options.py
+++ b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -767,11 +767,13 @@ def get_user_options(self, user: User):
             by_dbkey = {}
             for hda in hdas:
                 try:
-                    by_dbkey.update(self.hda_to_table_entries(hda, self.tool_data_table_name))
+                    table_entries = self.hda_to_table_entries(hda, self.tool_data_table_name)
                 except Exception as e:
                     # This is a bug, `hda_to_table_entries` is not generic enough for certain loc file
                     # structures, such as for the dada2_species, which doesn't have a dbkey column
+                    table_entries = {}
                     log.warning("Failed to read data table bundle entries: %s", e)
+                by_dbkey.update(table_entries)
             for data_table_entry in by_dbkey.values():
                 field_entry = []
                 for column_key in self.tool_data_table.columns.keys():