diff --git a/src/datachain/delta.py b/src/datachain/delta.py
index 125abd4fc..9ab20dd18 100644
--- a/src/datachain/delta.py
+++ b/src/datachain/delta.py
@@ -1,16 +1,12 @@
-import hashlib
 from collections.abc import Sequence
 from copy import copy
 from functools import wraps
 from typing import TYPE_CHECKING, TypeVar
 
-from attrs import frozen
-
 import datachain
 from datachain.dataset import DatasetDependency, DatasetRecord
 from datachain.error import DatasetNotFoundError
 from datachain.project import Project
-from datachain.query.dataset import Step, step_result
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -18,9 +14,7 @@
 
     from typing_extensions import ParamSpec
 
-    from datachain.catalog import Catalog
     from datachain.lib.dc import DataChain
-    from datachain.query.dataset import QueryGenerator
 
     P = ParamSpec("P")
 
@@ -49,38 +43,11 @@ def _inner(self: T, *args: "P.args", **kwargs: "P.kwargs") -> T:
     return _inner
 
 
-@frozen
-class _RegenerateSystemColumnsStep(Step):
-    catalog: "Catalog"
-
-    def hash_inputs(self) -> str:
-        return hashlib.sha256(b"regenerate_sys_columns").hexdigest()
-
-    def apply(self, query_generator: "QueryGenerator", temp_tables: list[str]):
-        selectable = query_generator.select()
-        regenerated = self.catalog.warehouse._regenerate_system_columns(
-            selectable,
-            keep_existing_columns=True,
-            regenerate_columns=None,
-        )
-
-        def q(*columns):
-            return regenerated.with_only_columns(*columns)
-
-        return step_result(q, regenerated.selected_columns)
-
-
 def _append_steps(dc: "DataChain", other: "DataChain"):
     """Returns cloned chain with appended steps from other chain.
     Steps are all those modification methods applied like filters, mappers etc.
     """
     dc = dc.clone()
-    dc._query.steps.append(
-        _RegenerateSystemColumnsStep(
-            catalog=dc.session.catalog,
-        )
-    )
-
     dc._query.steps += other._query.steps.copy()
     dc.signals_schema = other.signals_schema
     return dc
diff --git a/src/datachain/lib/dc/datasets.py b/src/datachain/lib/dc/datasets.py
index 3094882c7..d138d8eb6 100644
--- a/src/datachain/lib/dc/datasets.py
+++ b/src/datachain/lib/dc/datasets.py
@@ -200,6 +200,10 @@ def read_dataset(
         signals_schema |= SignalSchema.deserialize(query.feature_schema)
     else:
         signals_schema |= SignalSchema.from_column_types(query.column_types or {})
+
+    if delta:
+        signals_schema = signals_schema.clone_without_sys_signals()
+
     chain = DataChain(query, _settings, signals_schema)
 
     if delta:
diff --git a/src/datachain/lib/dc/storage.py b/src/datachain/lib/dc/storage.py
index 1fa3f4e95..09af40e51 100644
--- a/src/datachain/lib/dc/storage.py
+++ b/src/datachain/lib/dc/storage.py
@@ -187,6 +187,12 @@ def read_storage(
             project=listing_project_name,
             session=session,
             settings=settings,
+            delta=delta,
+            delta_on=delta_on,
+            delta_result_on=delta_result_on,
+            delta_compare=delta_compare,
+            delta_retry=delta_retry,
+            delta_unsafe=delta_unsafe,
         )
         dc._query.update = update
         dc.signals_schema = dc.signals_schema.mutate({f"{column}": file_type})
@@ -252,13 +258,4 @@ def lst_fn(ds_name, lst_uri):
 
     assert storage_chain is not None
 
-    if delta:
-        storage_chain = storage_chain._as_delta(
-            on=delta_on,
-            right_on=delta_result_on,
-            compare=delta_compare,
-            delta_retry=delta_retry,
-            delta_unsafe=delta_unsafe,
-        )
-
     return storage_chain
diff --git a/tests/func/test_delta.py b/tests/func/test_delta.py
index 8a08745ce..5e1e341a8 100644
--- a/tests/func/test_delta.py
+++ b/tests/func/test_delta.py
@@ -314,17 +314,66 @@ def build_chain(delta: bool):
 
     build_chain(delta=False).save(result_name)
 
-    build_chain(delta=True).save(
-        result_name,
-        delta=True,
-        delta_on="measurement_id",
-    )
+    build_chain(delta=True).save(result_name)
 
     assert set(
         dc.read_dataset(result_name, session=test_session).to_values("measurement_id")
     ) == {1, 2}
 
 
+def test_storage_delta_replay_regenerates_system_columns(test_session, tmp_dir):
+    data_dir = tmp_dir / f"regen_storage_{uuid.uuid4().hex[:8]}"
+    data_dir.mkdir()
+    storage_uri = data_dir.as_uri()
+    result_name = f"regen_storage_result_{uuid.uuid4().hex[:8]}"
+
+    def write_payload(index: int) -> None:
+        (data_dir / f"item{index}.txt").write_text(f"payload-{index}")
+
+    write_payload(1)
+    write_payload(2)
+
+    def build_chain(delta: bool):
+        read_kwargs = {"session": test_session, "update": True}
+        if delta:
+            read_kwargs |= {
+                "delta": True,
+                "delta_on": ["file.path"],
+                "delta_result_on": ["file.path"],
+            }
+
+        def get_measurement_id(file: File) -> int:
+            match = re.search(r"item(\d+)\.txt$", file.path)
+            assert match
+            return int(match.group(1))
+
+        def get_num(file: File) -> int:
+            return get_measurement_id(file)
+
+        chain = dc.read_storage(storage_uri, **read_kwargs)
+        return (
+            chain.mutate(num=1)
+            .select_except("num")
+            .map(measurement_id=get_measurement_id)
+            .map(err=lambda file: "")
+            .map(num=get_num)
+            .filter(C.err == "")
+            .select_except("err")
+            .map(double=lambda num: num * 2, output=int)
+            .select_except("num")
+        )
+
+    build_chain(delta=False).save(result_name)
+
+    write_payload(3)
+
+    build_chain(delta=True).save(result_name)
+
+    assert set(
+        dc.read_dataset(result_name, session=test_session).to_values("measurement_id")
+    ) == {1, 2, 3}
+
+
 def test_delta_update_from_storage(test_session, tmp_dir, tmp_path):
     ds_name = "delta_ds"
     path = tmp_dir.as_uri()