diff --git a/bottomless/src/replicator.rs b/bottomless/src/replicator.rs
index 633d8ff9..76a25f1b 100644
--- a/bottomless/src/replicator.rs
+++ b/bottomless/src/replicator.rs
@@ -1302,8 +1302,11 @@ impl Replicator {
             },
         };
 
-        tracing::info!("Restoring from generation {}", generation);
-        self.restore_from(generation, timestamp).await
+        let (action, recovered) = self.restore_from(generation, timestamp).await?;
+        tracing::info!(
+            "Restoring from generation {generation}: action={action:?}, recovered={recovered}"
+        );
+        Ok((action, recovered))
     }
 
     pub async fn get_last_consistent_frame(&self, generation: &Uuid) -> Result<u32> {
diff --git a/sqld/src/namespace/mod.rs b/sqld/src/namespace/mod.rs
index d54499b5..4861b7e5 100644
--- a/sqld/src/namespace/mod.rs
+++ b/sqld/src/namespace/mod.rs
@@ -657,6 +657,18 @@ impl Namespace<PrimaryDatabase> {
 
         tokio::fs::create_dir_all(&db_path).await?;
 
+        // FIXME: due to a bug in logger::checkpoint_db we call regular checkpointing code
+        // instead of our virtual WAL one. It's a bit tangled to fix right now, because
+        // we need WAL context for checkpointing, and WAL context needs the ReplicationLogger...
+        // So instead we checkpoint early, *before* bottomless gets initialized. That way
+        // we're sure bottomless won't try to back up any existing WAL frames and will instead
+        // treat the existing db file as the source of truth.
+        if config.bottomless_replication.is_some() {
+            tracing::debug!("Checkpointing before initializing bottomless");
+            crate::replication::primary::logger::checkpoint_db(&db_path.join("data"))?;
+            tracing::debug!("Checkpointed before initializing bottomless");
+        }
+
         let bottomless_replicator = if let Some(options) = &config.bottomless_replication {
             let options = make_bottomless_options(options, name.clone());
             let (replicator, did_recover) =
diff --git a/sqld/src/replication/primary/logger.rs b/sqld/src/replication/primary/logger.rs
index 9f69b876..580aa8e2 100644
--- a/sqld/src/replication/primary/logger.rs
+++ b/sqld/src/replication/primary/logger.rs
@@ -77,6 +77,7 @@ unsafe impl WalHook for ReplicationLoggerHook {
         assert_eq!(page_size, 4096);
         let wal_ptr = wal as *mut _;
         let last_valid_frame = wal.hdr.mxFrame;
+        tracing::trace!("Last valid frame before applying: {last_valid_frame}");
         let ctx = Self::wal_extract_ctx(wal);
 
         let mut frame_count = 0;
@@ -948,7 +949,9 @@ impl ReplicationLogger {
     }
 }
 
-fn checkpoint_db(data_path: &Path) -> anyhow::Result<()> {
+// FIXME: calling rusqlite::Connection's checkpoint here is a bug,
+// we need to always call our virtual WAL methods.
+pub fn checkpoint_db(data_path: &Path) -> anyhow::Result<()> {
     let wal_path = match data_path.parent() {
         Some(path) => path.join("data-wal"),
         None => return Ok(()),