MCP tools permanently removed from session after transient server disconnect, even after reconnection

Description

When an MCP server experiences a transient disconnect mid-conversation, Claude Code injects a system message permanently removing all tools from that server for the remainder of the session. Even if the server reconnects (confirmed via /mcp showing "connected"), the tools remain unavailable — ToolSearch returns no matches and the tools cannot be invoked.

Steps to reproduce

1. Start a Claude Code session with an MCP server configured (in this case, Notion OAuth-based MCP)
2. Use the MCP tools successfully for several interactions
3. Wait for a transient server disconnect (timeout, OAuth token refresh, process crash/restart)
4. Observe the system message: "The following deferred tools are no longer available (their MCP server disconnected). Do not search for them — ToolSearch will return no match"
5. Run /mcp — server shows as connected
6. Attempt to use ToolSearch to find the tools — returns no matches
7. Tools are permanently unavailable for the rest of the session

Expected behavior

If the MCP server reconnects successfully (as shown by /mcp), the tools should be re-injected into the active session's tool registry. A transient disconnect should not permanently remove tools.

Actual behavior

Tools are permanently removed from the conversation context. The only recovery is starting a new session.

Environment

• Platform: macOS (Darwin 25.2.0, Apple Silicon)
• MCP server type: Notion (OAuth-based, @anthropic-ai/mcp-notion)
• Claude Code version: current as of 2026-03-23
• Model: claude-opus-4-6

Impact

Mid-session loss of MCP tools forces users to abandon work-in-progress and start a new session. For long-running sessions with significant context built up, this is disruptive. The disconnect between /mcp status (connected) and actual tool availability (removed) is confusing.

Suggested fix

Either:

1. Re-inject tool definitions when a disconnected MCP server reconnects
2. Mark tools as temporarily unavailable (with retry) rather than permanently removed
3. Allow a /mcp refresh or similar command to re-register tools from connected servers