diff --git a/pylib/anki/collection.py b/pylib/anki/collection.py
index 098b69854..c3113fa9b 100644
--- a/pylib/anki/collection.py
+++ b/pylib/anki/collection.py
@@ -195,23 +195,17 @@ class Collection:
 
     flush = setMod
 
-    def modified_after_begin(self) -> bool:
+    def modified_by_backend(self) -> bool:
         # Until we can move away from long-running transactions, the Python
-        # code needs to know if transaction should be committed, so we need
+        # code needs to know if the transaction should be committed, so we need
         # to check if the backend updated the modification time.
         return self.db.last_begin_at != self.mod
 
     def save(self, name: Optional[str] = None, trx: bool = True) -> None:
         "Flush, commit DB, and take out another write lock if trx=True."
         # commit needed?
-        if self.db.modified_in_python or self.modified_after_begin():
-            if self.db.modified_in_python:
-                self.db.execute("update col set mod = ?", intTime(1000))
-                self.db.modified_in_python = False
-            else:
-                # modifications made by the backend will have already bumped
-                # mtime
-                pass
+        if self.db.modified_in_python or self.modified_by_backend():
+            self.db.modified_in_python = False
             self.db.commit()
             if trx:
                 self.db.begin()
diff --git a/rslib/src/backend/dbproxy.rs b/rslib/src/backend/dbproxy.rs
index 49207d334..d6d2b6f41 100644
--- a/rslib/src/backend/dbproxy.rs
+++ b/rslib/src/backend/dbproxy.rs
@@ -75,7 +75,7 @@ pub(super) fn db_command_bytes(col: &mut Collection, input: &[u8]) -> Result<Vec
             args,
             first_row_only,
         } => {
-            maybe_clear_undo(col, &sql);
+            update_state_after_modification(col, &sql);
             if first_row_only {
                 db_query_row(&col.storage, &sql, &args)?
             } else {
@@ -87,6 +87,10 @@ pub(super) fn db_command_bytes(col: &mut Collection, input: &[u8]) -> Result<Vec
             DBResult::None
         }
         DBRequest::Commit => {
+            if col.state.modified_by_dbproxy {
+                col.storage.set_modified()?;
+                col.state.modified_by_dbproxy = false;
+            }
             col.storage.commit_trx()?;
             DBResult::None
         }
@@ -96,17 +100,17 @@ pub(super) fn db_command_bytes(col: &mut Collection, input: &[u8]) -> Result<Vec
             DBResult::None
         }
         DBRequest::ExecuteMany { sql, args } => {
-            maybe_clear_undo(col, &sql);
+            update_state_after_modification(col, &sql);
             db_execute_many(&col.storage, &sql, &args)?
         }
     };
     Ok(serde_json::to_vec(&resp)?)
 }
 
-fn maybe_clear_undo(col: &mut Collection, sql: &str) {
+fn update_state_after_modification(col: &mut Collection, sql: &str) {
     if !is_dql(sql) {
         println!("clearing undo+study due to {}", sql);
-        col.discard_undo_and_study_queues();
+        col.update_state_after_dbproxy_modification();
     }
 }
 
diff --git a/rslib/src/collection.rs b/rslib/src/collection.rs
index bb701f9b6..2e664b087 100644
--- a/rslib/src/collection.rs
+++ b/rslib/src/collection.rs
@@ -65,6 +65,9 @@ pub struct CollectionState {
     pub(crate) notetype_cache: HashMap<NoteTypeID, Arc<NoteType>>,
     pub(crate) deck_cache: HashMap<DeckID, Arc<Deck>>,
     pub(crate) card_queues: Option<CardQueues>,
+    /// True if legacy Python code has executed SQL that has modified the
+    /// database, requiring modification time to be bumped.
+    pub(crate) modified_by_dbproxy: bool,
 }
 
 pub struct Collection {
@@ -92,7 +95,7 @@ impl Collection {
         let mut res = func(self);
 
         if res.is_ok() {
-            if let Err(e) = self.storage.mark_modified() {
+            if let Err(e) = self.storage.set_modified() {
                 res = Err(e);
             } else if let Err(e) = self.storage.commit_rust_trx() {
                 res = Err(e);
diff --git a/rslib/src/storage/sqlite.rs b/rslib/src/storage/sqlite.rs
index bbc0e0ff0..9d4d20c7e 100644
--- a/rslib/src/storage/sqlite.rs
+++ b/rslib/src/storage/sqlite.rs
@@ -257,7 +257,7 @@ impl SqliteStorage {
 
     //////////////////////////////////////////
 
-    pub(crate) fn mark_modified(&self) -> Result<()> {
+    pub(crate) fn set_modified(&self) -> Result<()> {
         self.set_modified_time(TimestampMillis::now())
     }
 
diff --git a/rslib/src/undo/mod.rs b/rslib/src/undo/mod.rs
index 339db290a..55a8d2449 100644
--- a/rslib/src/undo/mod.rs
+++ b/rslib/src/undo/mod.rs
@@ -174,6 +174,11 @@ impl Collection {
         self.clear_study_queues();
     }
 
+    pub(crate) fn update_state_after_dbproxy_modification(&mut self) {
+        self.discard_undo_and_study_queues();
+        self.state.modified_by_dbproxy = true;
+    }
+
     #[inline]
     pub(crate) fn save_undo(&mut self, item: impl Into<UndoableChange>) {
         self.state.undo.save(item.into());