diff --git a/erpnext/controllers/queries.py b/erpnext/controllers/queries.py
index 919bbb477f4..463cb859970 100644
--- a/erpnext/controllers/queries.py
+++ b/erpnext/controllers/queries.py
@@ -415,7 +415,6 @@ def get_batches_from_stock_ledger_entries(searchfields, txt, filters, start=0, p
 			stock_ledger_entry.batch_no,
 			Sum(stock_ledger_entry.actual_qty).as_("qty"),
 		)
-		.where((batch_table.expiry_date >= expiry_date) | (batch_table.expiry_date.isnull()))
 		.where(stock_ledger_entry.is_cancelled == 0)
 		.where(
 			(stock_ledger_entry.item_code == filters.get("item_code"))
@@ -428,6 +427,9 @@ def get_batches_from_stock_ledger_entries(searchfields, txt, filters, start=0, p
 		.limit(page_len)
 	)
 
+	if not filters.get("include_expired_batches"):
+		query = query.where((batch_table.expiry_date >= expiry_date) | (batch_table.expiry_date.isnull()))
+
 	query = query.select(
 		Concat("MFG-", batch_table.manufacturing_date).as_("manufacturing_date"),
 		Concat("EXP-", batch_table.expiry_date).as_("expiry_date"),
@@ -466,7 +468,6 @@ def get_batches_from_serial_and_batch_bundle(searchfields, txt, filters, start=0
 			bundle.batch_no,
 			Sum(bundle.qty).as_("qty"),
 		)
-		.where((batch_table.expiry_date >= expiry_date) | (batch_table.expiry_date.isnull()))
 		.where(stock_ledger_entry.is_cancelled == 0)
 		.where(
 			(stock_ledger_entry.item_code == filters.get("item_code"))
@@ -479,6 +480,11 @@ def get_batches_from_serial_and_batch_bundle(searchfields, txt, filters, start=0
 		.limit(page_len)
 	)
 
+	if not filters.get("include_expired_batches"):
+		bundle_query = bundle_query.where(
+			(batch_table.expiry_date >= expiry_date) | (batch_table.expiry_date.isnull())
+		)
+
 	bundle_query = bundle_query.select(
 		Concat("MFG-", batch_table.manufacturing_date),
 		Concat("EXP-", batch_table.expiry_date),
diff --git a/erpnext/public/js/utils/serial_no_batch_selector.js b/erpnext/public/js/utils/serial_no_batch_selector.js
index 61b40d6fef0..de1faf36ef5 100644
--- a/erpnext/public/js/utils/serial_no_batch_selector.js
+++ b/erpnext/public/js/utils/serial_no_batch_selector.js
@@ -462,6 +462,8 @@ erpnext.SerialBatchPackageSelector = class SerialNoBatchBundleUpdate {
 							is_inward = true;
 						}
 
+						let include_expired_batches = me.include_expired_batches();
+
 						return {
 							query: "erpnext.controllers.queries.get_batch_no",
 							filters: {
@@ -469,6 +471,7 @@ erpnext.SerialBatchPackageSelector = class SerialNoBatchBundleUpdate {
 								warehouse:
 									this.item.s_warehouse || this.item.t_warehouse || this.item.warehouse,
 								is_inward: is_inward,
+								include_expired_batches: include_expired_batches,
 							},
 						};
 					},
@@ -497,6 +500,14 @@ erpnext.SerialBatchPackageSelector = class SerialNoBatchBundleUpdate {
 		return fields;
 	}
 
+	include_expired_batches() {
+		return (
+			this.frm.doc.doctype === "Stock Reconciliation" ||
+			(this.frm.doc.doctype === "Stock Entry" &&
+				["Material Receipt", "Material Transfer", "Material Issue"].includes(this.frm.doc.purpose))
+		);
+	}
+
 	get_auto_data() {
 		let { qty, based_on } = this.dialog.get_values();
 
diff --git a/erpnext/stock/doctype/serial_and_batch_bundle/serial_and_batch_bundle.py b/erpnext/stock/doctype/serial_and_batch_bundle/serial_and_batch_bundle.py
index ed6d5e155d7..08aa978aa99 100644
--- a/erpnext/stock/doctype/serial_and_batch_bundle/serial_and_batch_bundle.py
+++ b/erpnext/stock/doctype/serial_and_batch_bundle/serial_and_batch_bundle.py
@@ -689,6 +689,9 @@ class SerialandBatchBundle(Document):
 		serial_batches = {}
 		for row in self.entries:
 			if not row.qty and row.batch_no and not row.serial_no:
+				if self.voucher_type == "Stock Reconciliation" and self.type_of_transaction == "Inward":
+					continue
+
 				frappe.throw(
 					_("At row {0}: Qty is mandatory for the batch {1}").format(
 						bold(row.idx), bold(row.batch_no)
diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.js b/erpnext/stock/doctype/stock_entry/stock_entry.js
index ea47ffd79ea..0e39c2a9756 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.js
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.js
@@ -117,6 +117,10 @@ frappe.ui.form.on("Stock Entry", {
 					filters["is_inward"] = 1;
 				}
 
+				if (["Material Receipt", "Material Transfer", "Material Issue"].includes(doc.purpose)) {
+					filters["include_expired_batches"] = 1;
+				}
+
 				return {
 					query: "erpnext.controllers.queries.get_batch_no",
 					filters: filters,
diff --git a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
index 8ee3d9b3901..f671c11712a 100644
--- a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
+++ b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
@@ -324,6 +324,7 @@ class StockReconciliation(StockController):
 				row.item_code,
 				posting_date=self.posting_date,
 				posting_time=self.posting_time,
+				for_stock_levels=True,
 			)
 
 			total_current_qty += current_qty
@@ -1322,7 +1323,16 @@ def get_stock_balance_for(
 		qty, rate = data
 
 	if item_dict.get("has_batch_no"):
-		qty = get_batch_qty(batch_no, warehouse, posting_date=posting_date, posting_time=posting_time) or 0
+		qty = (
+			get_batch_qty(
+				batch_no,
+				warehouse,
+				posting_date=posting_date,
+				posting_time=posting_time,
+				for_stock_levels=True,
+			)
+			or 0
+		)
 
 	return {
 		"qty": qty,
diff --git a/erpnext/stock/serial_batch_bundle.py b/erpnext/stock/serial_batch_bundle.py
index c1002095b62..cb156aea119 100644
--- a/erpnext/stock/serial_batch_bundle.py
+++ b/erpnext/stock/serial_batch_bundle.py
@@ -124,7 +124,7 @@ class SerialBatchBundle:
 			"Outward": self.sle.actual_qty < 0,
 		}.get(sn_doc.type_of_transaction)
 
-		if not condition:
+		if not condition and self.sle.actual_qty:
 			correct_type = "Inward"
 			if sn_doc.type_of_transaction == "Inward":
 				correct_type = "Outward"
@@ -133,7 +133,7 @@ class SerialBatchBundle:
 			frappe.throw(_(msg), title=_("Incorrect Type of Transaction"))
 
 		precision = sn_doc.precision("total_qty")
-		if flt(sn_doc.total_qty, precision) != flt(self.sle.actual_qty, precision):
+		if self.sle.actual_qty and flt(sn_doc.total_qty, precision) != flt(self.sle.actual_qty, precision):
 			msg = f"Total qty {flt(sn_doc.total_qty, precision)} of Serial and Batch Bundle {link} is not equal to Actual Qty {flt(self.sle.actual_qty, precision)} in the {self.sle.voucher_type} {self.sle.voucher_no}"
 			frappe.throw(_(msg))
 
diff --git a/erpnext/stock/stock_ledger.py b/erpnext/stock/stock_ledger.py
index ccf7c7643c8..26e7af150b9 100644
--- a/erpnext/stock/stock_ledger.py
+++ b/erpnext/stock/stock_ledger.py
@@ -1183,6 +1183,7 @@ class update_entries_after:
 		stock_entry.calculate_rate_and_amount(reset_outgoing_rate=False, raise_error_if_no_rate=False)
 		stock_entry.db_update()
 		for d in stock_entry.items:
+			# Update only the row that matches the voucher_detail_no or the row containing the FG/Scrap Item.
 			if d.name == voucher_detail_no or (not d.s_warehouse and d.t_warehouse):
 				d.db_update()