diff --git a/agent/conversation_compression.py b/agent/conversation_compression.py
index 1b6cca41a9..c25a0c2d4e 100644
--- a/agent/conversation_compression.py
+++ b/agent/conversation_compression.py
@@ -3143,6 +3143,17 @@ def _fold_todo_snapshot(agent: Any, compressed: list) -> None:
 
 def _rebuild_system_prompt_at_boundary(agent: Any, system_message: str) -> str:
     """Refresh tool schemas and rebuild the system prompt at the commit boundary."""
+    if getattr(agent, "_retain_seeded_system_prompt", False) is True:
+        # Gateway hygiene / gateway /compress run a detached agent with a reduced toolset and no live
+        # surface: its builder output drops the skills index, external provider blocks and tool guidance,
+        # and the commit below would persist that over the live session's snapshot (restored verbatim by
+        # the next fresh agent). Keep the seeded bytes; the live agent's own compaction propagates updates.
+        seeded_system_prompt = agent._cached_system_prompt or ""
+        agent._cached_system_prompt = seeded_system_prompt
+        if seeded_system_prompt:
+            from agent.system_prompt import reconstruct_static_prefix
+            reconstruct_static_prefix(agent, system_message=system_message, log_label="compression seeded-prompt")
+        return seeded_system_prompt
     cached_system_prompt = agent._cached_system_prompt
     agent._invalidate_system_prompt()
 
diff --git a/gateway/run.py b/gateway/run.py
index d38fbd0978..78c0de2ec5 100644
--- a/gateway/run.py
+++ b/gateway/run.py
@@ -509,6 +509,8 @@ def _seed_hygiene_system_prompt(agent: Any, session_row: Optional[Dict[str, Any]
             stored_prompt = raw_prompt
 
     agent._cached_system_prompt = stored_prompt
+    # Compaction otherwise rebuilds the prompt at the commit boundary from this agent's reduced toolset.
+    agent._retain_seeded_system_prompt = True
     return bool(stored_prompt)
 
 
diff --git a/tests/gateway/test_hygiene_compaction_keeps_seeded_prompt.py b/tests/gateway/test_hygiene_compaction_keeps_seeded_prompt.py
new file mode 100644
index 0000000000..78ce8a33e9
--- /dev/null
+++ b/tests/gateway/test_hygiene_compaction_keeps_seeded_prompt.py
@@ -0,0 +1,64 @@
+"""Gateway hygiene / gateway /compress must not persist a reduced-toolset prompt over a live session.
+
+Both paths compact with a detached ``AIAgent(enabled_toolsets=["memory"])`` seeded with the session's
+stored prompt (``_seed_hygiene_system_prompt``). Compaction rebuilds the prompt at the commit boundary
+(#98426) and the commit persists the result, so without the seed being honoured the session row lost the
+skills index / provider blocks and every later fresh agent restored those degraded bytes verbatim.
+"""
+from types import SimpleNamespace
+from unittest.mock import patch
+
+from agent import conversation_compression as cc
+from gateway.run import _seed_hygiene_system_prompt
+
+STORED = "You are Hermes.\n\n## Skills (mandatory)\n<available_skills>\n- a: b\n</available_skills>"
+DEGRADED = "You are Hermes."
+
+
+def _agent(**over):
+    built = []
+
+    def _build(system_message=None):
+        built.append(system_message)
+        return DEGRADED
+
+    def _invalidate():
+        agent._cached_system_prompt = None
+
+    fields = dict(_cached_system_prompt=None, session_id="sess-1",
+                  _build_system_prompt=_build, _invalidate_system_prompt=_invalidate)
+    fields.update(over)
+    agent = SimpleNamespace(**fields)
+    return agent, built
+
+
+def _rebuild(agent):
+    with patch.object(cc, "_refresh_agent_tool_definitions", return_value=False), \
+         patch("agent.system_prompt.reconstruct_static_prefix"):
+        return cc._rebuild_system_prompt_at_boundary(agent, "")
+
+
+def test_seeded_hygiene_agent_keeps_the_stored_prompt_at_the_commit_boundary():
+    agent, built = _agent()
+    assert _seed_hygiene_system_prompt(agent, {"system_prompt": STORED}) is True
+
+    result = _rebuild(agent)
+
+    assert result is STORED
+    assert agent._cached_system_prompt is STORED
+    assert built == []
+
+
+def test_seed_without_a_stored_prompt_persists_empty_not_the_reduced_build():
+    agent, built = _agent()
+    assert _seed_hygiene_system_prompt(agent, None) is False
+
+    assert _rebuild(agent) == ""
+    assert built == []
+
+
+def test_live_agent_compaction_still_rebuilds():
+    agent, built = _agent(_cached_system_prompt=STORED)
+
+    assert _rebuild(agent) == DEGRADED
+    assert built == [""]