diff --git a/flattentool/json_input.py b/flattentool/json_input.py
index e1cc6a1..8b737ff 100644
--- a/flattentool/json_input.py
+++ b/flattentool/json_input.py
@@ -161,12 +161,11 @@ def __init__(
             self.main_sheet = PersistentSheet.from_sheet(
                 schema_parser.main_sheet, self.connection
             )
-            for sheet_name, sheet in list(self.sub_sheets.items()):
+            for sheet_name, sheet in list(schema_parser.sub_sheets.items()):
                 self.sub_sheets[sheet_name] = PersistentSheet.from_sheet(
                     sheet, self.connection
                 )
 
-            self.sub_sheets = copy.deepcopy(schema_parser.sub_sheets)
             if remove_empty_schema_columns:
                 # Don't use columns from the schema parser
                 # (avoids empty columns)
@@ -312,7 +311,7 @@ def parse(self):
         if self.remove_empty_schema_columns:
             # Remove sheets with no lines of data
             for sheet_name, sheet in list(self.sub_sheets.items()):
-                if not sheet.lines:
+                if not sheet.line_count:
                     del self.sub_sheets[sheet_name]
 
         if self.preserve_fields_input:
diff --git a/flattentool/sheet.py b/flattentool/sheet.py
index 48d7a98..2531f5f 100644
--- a/flattentool/sheet.py
+++ b/flattentool/sheet.py
@@ -21,6 +21,10 @@ def __init__(self, columns=None, root_id="", name=None):
     def lines(self):
         return self._lines
 
+    @property
+    def line_count(self):
+        return len(self._lines)
+
     def add_field(self, field, id_field=False):
         columns = self.id_columns if id_field else self.columns
         if field not in columns:
@@ -65,6 +69,10 @@ def lines(self):
                 self.connection.cacheMinimize()
             yield value
 
+    @property
+    def line_count(self):
+        return self.index
+
     def append_line(self, flattened_dict):
         self.connection.root.sheet_store[self.name][self.index] = flattened_dict
         self.index += 1
diff --git a/flattentool/tests/test_json_input.py b/flattentool/tests/test_json_input.py
index 3535786..b9e067e 100644
--- a/flattentool/tests/test_json_input.py
+++ b/flattentool/tests/test_json_input.py
@@ -327,7 +327,7 @@ def test_sub_sheets(self, tmpdir, remove_empty_schema_columns):
             assert list(parser.sub_sheets["g"]) == list(["ocid", "g/0/h"])
         else:
             assert list(parser.sub_sheets["c"]) == list(["ocid", "c/0/d"])
-        assert parser.sub_sheets["c"].lines == [{"c/0/d": "e"}]
+        assert list(parser.sub_sheets["c"].lines) == [{"c/0/d": "e"}]
 
     def test_column_matching(self, tmpdir):
         test_schema = tmpdir.join("test.json")
@@ -387,7 +387,7 @@ def test_rollup(self):
         assert set(parser.sub_sheets["testA"]) == set(
             ["ocid", "testA/0/testB", "testA/0/testC"]
         )
-        assert parser.sub_sheets["testA"].lines == [
+        assert list(parser.sub_sheets["testA"].lines) == [
             {"testA/0/testB": "1", "testA/0/testC": "2"}
         ]
 
@@ -438,7 +438,7 @@ def test_rollup_multiple_values(self, recwarn):
         assert set(parser.sub_sheets["testA"]) == set(
             ["testA/0/testB", "testA/0/testC"]
         )
-        assert parser.sub_sheets["testA"].lines == [
+        assert list(parser.sub_sheets["testA"].lines) == [
             {"testA/0/testB": "1", "testA/0/testC": "2"},
             {"testA/0/testB": "3", "testA/0/testC": "4"},
         ]