diff --git a/lib/galaxy/tools/lazy_toolbox.py b/lib/galaxy/tools/lazy_toolbox.py
index 17c3992f99d..1bb0e812b3e 100644
--- a/lib/galaxy/tools/lazy_toolbox.py
+++ b/lib/galaxy/tools/lazy_toolbox.py
@@ -708,16 +708,29 @@ class LazyToolBox(ToolBox):
         return [placement for placement in placements if placement.tool_id in keep]
 
     def _latest_panel_tool_ids(self, tool_ids: list[str]) -> list[str]:
+        """Collapse each lineage's placements to its newest version's id.
+
+        Hidden and visible entries collapse independently (the lineage key
+        carries ``entry.hidden``): :meth:`_place_stub` mirrors every
+        placement into the integrated panel — hidden included — but only
+        visible ones into the live panel. Dropping hidden entries here (as an
+        earlier revision did) kept their placements from ever reaching
+        ``_place_stub``, so a fast-path boot persisted
+        ``integrated_tool_panel.xml`` without hidden tools, losing their
+        positions. Keeping the latest hidden lineage member routes its
+        placement to the integrated projection while a visible sibling in the
+        same lineage still reaches the live panel.
+        """
         if self._tool_index is None:
             return tool_ids
-        ordered_lineages: list[tuple[str | None, str]] = []
-        latest_by_lineage: dict[tuple[str | None, str], ToolIndexEntry] = {}
+        ordered_lineages: list[tuple[str | None, str, bool]] = []
+        latest_by_lineage: dict[tuple[str | None, str, bool], ToolIndexEntry] = {}
         for tool_id in tool_ids:
             entry = self._tool_index.entries.get(tool_id)
-            if entry is None or entry.hidden:
+            if entry is None:
                 continue
             lineage_id = remove_version_from_guid(entry.id) or entry.id
-            lineage_key = (entry.panel_section_id, lineage_id)
+            lineage_key = (entry.panel_section_id, lineage_id, entry.hidden)
             current = latest_by_lineage.get(lineage_key)
             if current is None:
                 ordered_lineages.append(lineage_key)
diff --git a/test/unit/app/tools/test_lazy_tool.py b/test/unit/app/tools/test_lazy_tool.py
index c23dc4e6581..1680f98ec90 100644
--- a/test/unit/app/tools/test_lazy_tool.py
+++ b/test/unit/app/tools/test_lazy_tool.py
@@ -715,3 +715,28 @@ def test_invalidate_index_cache_keeps_materialised_tool_when_content_unchanged()
     box.invalidate_index_cache()
 
     assert box.get_tool("tool1") is original
+
+
+def test_fast_path_places_hidden_entry_in_integrated_panel_only():
+    box = _registry_box()
+    visible = _entry(
+        id="visible_tool", version="1.0", hidden=False, panel_section_id="sec1", panel_section_name="Section 1"
+    )
+    hidden = _entry(
+        id="hidden_tool", version="1.0", hidden=True, panel_section_id="sec1", panel_section_name="Section 1"
+    )
+    box._tool_index.add_entry(visible)
+    box._tool_index.add_entry(hidden)
+
+    placements = box._index_panel_items()
+    assert {p.tool_id for p in placements} == {"visible_tool", "hidden_tool"}
+    for placement in placements:
+        stub = box._register_lazy_entry(box._tool_index.entries[placement.tool_id], place_in_panel=False)
+        box._place_stub(stub, placement.section_id, placement.section_name, hidden=placement.hidden)
+
+    integrated = box._integrated_tool_panel["sec1"].elems
+    assert integrated.has_tool_with_id("hidden_tool")
+    assert integrated.has_tool_with_id("visible_tool")
+    live = box._tool_panel["sec1"].elems
+    assert live.has_tool_with_id("visible_tool")
+    assert not live.has_tool_with_id("hidden_tool")