diff --git a/rust/Cargo.lock b/rust/Cargo.lock
index 13745d90..1e4ba983 100644
--- a/rust/Cargo.lock
+++ b/rust/Cargo.lock
@@ -118,6 +118,7 @@ dependencies = [
  "devkit-core",
  "devkit-harness",
  "libc",
+ "rusqlite",
  "serde",
  "serde_json",
  "tokio",
diff --git a/rust/crates/devkit-core/src/discover.rs b/rust/crates/devkit-core/src/discover.rs
index 5cdb502c..f61dcf03 100644
--- a/rust/crates/devkit-core/src/discover.rs
+++ b/rust/crates/devkit-core/src/discover.rs
@@ -292,6 +292,16 @@ fn local_utc_offset_secs(utc_secs: i64) -> i64 {
     }
 }
 
+/// Process liveness: exists or permission-denied (EPERM = exists, not ours).
+pub fn pid_alive(pid: i64) -> bool {
+    unsafe {
+        if libc::kill(pid as libc::pid_t, 0) == 0 {
+            return true;
+        }
+    }
+    std::io::Error::last_os_error().raw_os_error() == Some(libc::EPERM)
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
diff --git a/rust/crates/devkit-core/src/store/registry.rs b/rust/crates/devkit-core/src/store/registry.rs
index 61d4e11a..929f9c17 100644
--- a/rust/crates/devkit-core/src/store/registry.rs
+++ b/rust/crates/devkit-core/src/store/registry.rs
@@ -268,10 +268,21 @@ impl Store {
     /// start-time name check.
     pub fn prune_dead(&self) -> Result<usize> {
         let conn = self.conn.lock().unwrap();
-        Ok(conn.execute(
-            "DELETE FROM agents WHERE name IS NOT NULL AND gone_at IS NOT NULL",
-            [],
-        )?)
+        let pids: Vec<i64> = conn
+            .prepare("SELECT pid FROM agents WHERE name IS NOT NULL AND gone_at IS NOT NULL")?
+            .query_map([], |r| r.get(0))?
+            .filter_map(|r| r.ok())
+            .collect();
+        // gone_at is sweep bookkeeping — prune only tombstones whose pid is
+        // actually dead. A tombstoned-but-alive row keeps its registration;
+        // deleting it would free a name that is still in use.
+        let mut n = 0;
+        for pid in pids {
+            if !crate::discover::pid_alive(pid) {
+                n += conn.execute("DELETE FROM agents WHERE pid=?1", params![pid])?;
+            }
+        }
+        Ok(n)
     }
 
     /// Registry overlays for live rows: pid -> (name, pinned). Tombstones
@@ -384,8 +395,10 @@ mod tests {
     #[test]
     fn tombstone_frees_name_via_prune_and_reuse() {
         let (s, _p) = tmp_store();
-        s.apply_agent_snapshot(&[proc_started(10, 1000)]).unwrap();
-        s.register_start(10, "my-agent", "codex", "/tmp", "tmux", &json!({}))
+        // i32::MAX is above every pid_max — guaranteed dead (pid 10 is a
+        // live kernel thread on Linux CI, which kept the tombstone alive).
+        s.apply_agent_snapshot(&[proc_started(i32::MAX as i64, 1000)]).unwrap();
+        s.register_start(i32::MAX as i64, "my-agent", "codex", "/tmp", "tmux", &json!({}))
             .unwrap();
         s.apply_agent_snapshot(&[]).unwrap();
         // Dead name does not block a new start once pruned.
diff --git a/rust/crates/devkitd/Cargo.toml b/rust/crates/devkitd/Cargo.toml
index 4cffc6ee..10229a7d 100644
--- a/rust/crates/devkitd/Cargo.toml
+++ b/rust/crates/devkitd/Cargo.toml
@@ -14,3 +14,6 @@ libc.workspace = true
 tracing.workspace = true
 tracing-subscriber.workspace = true
 serde.workspace = true
+
+[dev-dependencies]
+rusqlite.workspace = true
diff --git a/rust/crates/devkitd/src/rpc/agent.rs b/rust/crates/devkitd/src/rpc/agent.rs
index 8235e31e..46c29e36 100644
--- a/rust/crates/devkitd/src/rpc/agent.rs
+++ b/rust/crates/devkitd/src/rpc/agent.rs
@@ -52,12 +52,5 @@ fn base36(mut n: i64) -> String {
     out.iter().rev().map(|c| *c as char).collect()
 }
 
-/// Process liveness: exists or permission-denied (EPERM = exists, not ours).
-pub(super) fn pid_alive(pid: i64) -> bool {
-    unsafe {
-        if libc::kill(pid as libc::pid_t, 0) == 0 {
-            return true;
-        }
-    }
-    std::io::Error::last_os_error().raw_os_error() == Some(libc::EPERM)
-}
+/// Process liveness lives in devkit-core (prune_dead needs it too).
+pub(super) use devkit_core::discover::pid_alive;
diff --git a/rust/crates/devkitd/src/rpc/agent/start.rs b/rust/crates/devkitd/src/rpc/agent/start.rs
index 587cb206..3bb5e40a 100644
--- a/rust/crates/devkitd/src/rpc/agent/start.rs
+++ b/rust/crates/devkitd/src/rpc/agent/start.rs
@@ -72,12 +72,22 @@ pub fn run_with(
     let _start_guard = daemon.start_mutex.lock().unwrap();
 
     daemon.store.prune_dead().map_err(RpcError::internal)?;
+    // Re-sync the legacy registry inside the mutex — agents started via the
+    // fallback path (or before daemon boot) live only in agents.db until
+    // this delta-merge; the name check must see them.
+    daemon
+        .store
+        .import_legacy_agents()
+        .map_err(RpcError::internal)?;
     if let Some(existing) = daemon
         .store
         .lookup_name(&name)
         .map_err(RpcError::internal)?
     {
-        if pid_alive(existing.pid) && existing.gone_at.is_none() {
+        // Live pid = in use, whatever gone_at says: a tombstone is sweep
+        // bookkeeping, not proof of death (imported legacy rows are
+        // tombstoned-by-default while their pids run fine).
+        if pid_alive(existing.pid) {
             return Err(RpcError::new(
                 "name_in_use",
                 format!(
@@ -289,6 +299,56 @@ mod tests {
         assert!(valid_agent_name(&n), "generated name must validate");
     }
 
+    #[test]
+    fn tombstoned_but_live_pid_still_blocks_name() {
+        // gone_at is sweep bookkeeping — a tombstone whose pid is alive
+        // (imported legacy row, or a process the sweep hasn't re-seen) must
+        // still block the name.
+        let f = FixtureDir::new("tomb-live");
+        let d = daemon(&f);
+        let self_pid = std::process::id() as i64;
+        d.store
+            .register_start(self_pid, "my-agent", "claude", "/tmp", "tmux", &json!({}))
+            .unwrap();
+        d.store.apply_agent_snapshot(&[]).unwrap(); // tombstones the row
+        let reg = d.store.lookup_name("my-agent").unwrap().unwrap();
+        assert!(reg.gone_at.is_some());
+        let e = run_with(&d, params(Some("my-agent"), "/tmp"), &runtimes(&f)).unwrap_err();
+        assert_eq!(e.code, "name_in_use");
+    }
+
+    #[test]
+    fn legacy_row_written_after_daemon_boot_blocks_name() {
+        // An agent started via the fallback path registers only in
+        // agents.db — the start path must re-import before the name check.
+        let f = FixtureDir::new("legacy-post-boot");
+        let d = daemon(&f);
+        let self_pid = std::process::id() as i64;
+        let legacy = f.0.join("agents.db");
+        let conn = rusqlite::Connection::open(&legacy).unwrap();
+        conn.execute_batch(
+            "CREATE TABLE agents (
+                type TEXT NOT NULL, pid INTEGER NOT NULL, name TEXT NOT NULL UNIQUE,
+                tmux_session TEXT NOT NULL DEFAULT '', cwd TEXT NOT NULL DEFAULT '',
+                started_at TEXT NOT NULL, session_id TEXT NOT NULL DEFAULT '',
+                session_file_path TEXT NOT NULL DEFAULT '', updated_at TEXT NOT NULL,
+                pinned INTEGER NOT NULL DEFAULT 0, runtime TEXT NOT NULL DEFAULT 'tmux',
+                runtime_ref TEXT NOT NULL DEFAULT '',
+                PRIMARY KEY (type, pid));",
+        )
+        .unwrap();
+        conn.execute(
+            "INSERT INTO agents (type,pid,name,cwd,started_at,updated_at,runtime,runtime_ref)
+             VALUES ('claude',?1,'claude-1','/tmp','2026-10-16T00:00:00.000Z',
+                     '2026-10-16T00:00:00.000Z','tmux','{\"session\":\"claude-1\"}')",
+            rusqlite::params![self_pid],
+        )
+        .unwrap();
+        d.store.set_legacy_db(legacy).unwrap();
+        let e = run_with(&d, params(Some("claude-1"), "/tmp"), &runtimes(&f)).unwrap_err();
+        assert_eq!(e.code, "name_in_use");
+    }
+
     #[test]
     fn started_event_payload_is_serializable_result() {
         let f = FixtureDir::new("payload");