Separate tracking. Tag costs as direct to zero-rated sales, direct to standard-rated sales, or overheads (apportion overheads by a reasonable method).
Refund or carry-forward?- Refund is realistic when input VAT regularly exceeds output VAT (e.g., exporters with large freight/warehouse costs).
- Carry-forward may be simpler if the amount is small or you expect near-term output VAT to offset it.
Evidence for recovery: Valid Tax Invoices from suppliers, proof of payment (if requested), and a memo explaining your apportionment method.