diff --git a/test/unit/app/tools/source_store/test_sqlite_store.py b/test/unit/app/tools/source_store/test_sqlite_store.py
index fafbce03710..c4d71b5286d 100644
--- a/test/unit/app/tools/source_store/test_sqlite_store.py
+++ b/test/unit/app/tools/source_store/test_sqlite_store.py
@@ -5,6 +5,7 @@ import tempfile
 
 import pytest
 
+import galaxy.tools.source_store.sqlalchemy as sqlalchemy_store_module
 from galaxy.tools.source_store import (
     ReadOnlyStoreError,
     StoredToolSource,
@@ -75,6 +76,18 @@ def test_index_round_trip(sqlite_path):
     assert loaded.entries["t1"].name == "T1"
 
 
+def test_load_index_discards_stale_schema(sqlite_path, monkeypatch):
+    store = SqliteToolSourceStore(url=_sqlite_url(sqlite_path))
+    store.store_index(ToolIndex(entries={"t1": ToolIndexEntry(id="t1", name="T1")}))
+
+    # Simulate a Galaxy upgrade that changed the ToolIndex model: the
+    # persisted blob's stamp no longer matches, so the store must report "no
+    # index" (triggering a rebuild) rather than load stale/defaulted fields.
+    monkeypatch.setattr(sqlalchemy_store_module, "INDEX_SCHEMA_HASH", "post-upgrade-schema-hash")
+    fresh = SqliteToolSourceStore(url=_sqlite_url(sqlite_path))
+    assert fresh.load_index() is None
+
+
 def test_read_only_refuses_writes(sqlite_path):
     rw = SqliteToolSourceStore(url=_sqlite_url(sqlite_path))
     rw.store(_source())
diff --git a/tool-data/shed/bwa_mem_index.loc b/tool-data/shed/bwa_mem_index.loc
index d4c10ceadcd..6c75d73a7bc 100644
--- a/tool-data/shed/bwa_mem_index.loc
+++ b/tool-data/shed/bwa_mem_index.loc
@@ -7,8 +7,8 @@
 #
 #<unique_build_id>   <dbkey>   <display_name>   <file_path>
 #
-#So, for example, if you had phiX indexed stored in 
-#/depot/data2/galaxy/phiX/base/, 
+#So, for example, if you had phiX indexed stored in
+#/depot/data2/galaxy/phiX/base/,
 #then the bwa_index.loc entry would look like this:
 #
 #phiX174   phiX   phiX Pretty   /depot/data2/galaxy/phiX/base/phiX.fa
diff --git a/tool-data/shed/bwa_mem_index.loc.sample b/tool-data/shed/bwa_mem_index.loc.sample
index d4c10ceadcd..6c75d73a7bc 100644
--- a/tool-data/shed/bwa_mem_index.loc.sample
+++ b/tool-data/shed/bwa_mem_index.loc.sample
@@ -7,8 +7,8 @@
 #
 #<unique_build_id>   <dbkey>   <display_name>   <file_path>
 #
-#So, for example, if you had phiX indexed stored in 
-#/depot/data2/galaxy/phiX/base/, 
+#So, for example, if you had phiX indexed stored in
+#/depot/data2/galaxy/phiX/base/,
 #then the bwa_index.loc entry would look like this:
 #
 #phiX174   phiX   phiX Pretty   /depot/data2/galaxy/phiX/base/phiX.fa